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- PDB-6olg: Human ribosome nascent chain complex stalled by a drug-like small... -

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Basic information

Entry
Database: PDB / ID: 6olg
TitleHuman ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA)
Components
  • (40S ribosomal protein ...) x 32
  • (60S ribosomal protein ...) x 44
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • Cadherin-1
  • Receptor of activated protein C kinase 1
  • mRNAMessenger RNA
  • tRNATransfer RNA
KeywordsRIBOSOME / selective stalling / drug-like molecule / human ribosome nascent chain complex
Function / homology
Function and homology information


embryonic brain development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / regulation of translation at presynapse, modulating synaptic transmission / negative regulation of formation of translation preinitiation complex / positive regulation of selenocysteine incorporation / optic nerve development / eukaryotic 80S initiation complex / negative regulation of protein neddylation / 5.8S rRNA binding / TORC2 complex binding ...embryonic brain development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / regulation of translation at presynapse, modulating synaptic transmission / negative regulation of formation of translation preinitiation complex / positive regulation of selenocysteine incorporation / optic nerve development / eukaryotic 80S initiation complex / negative regulation of protein neddylation / 5.8S rRNA binding / TORC2 complex binding / positive regulation of signal transduction by p53 class mediator / axial mesoderm development / ribosomal protein import into nucleus / protein-DNA complex disassembly / middle ear morphogenesis / 90S preribosome assembly / flotillin complex / selenocysteine insertion sequence binding / gamma-catenin binding / GAIT complex / pituitary gland development / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / response to extracellular stimulus / exit from mitosis / negative regulation of RNA splicing / cellular response to indole-3-methanol / IRE1-RACK1-PP2A complex / ubiquitin ligase inhibitor activity / laminin receptor activity / retinal ganglion cell axon guidance / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of cell division / regulation of translation involved in cellular response to UV / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / alpha-beta T cell differentiation / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of hydrogen peroxide-induced neuron death / A band / negative regulation of DNA repair / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / negative regulation of ubiquitin protein ligase activity / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of ceramide biosynthetic process / erythrocyte homeostasis / cellular response to lithium ion / catenin complex / ankyrin binding / mammalian oogenesis stage / NF-kappaB complex / negative regulation of phagocytosis / apical junction complex / cytosolic ribosome / regulation of establishment of cell polarity / positive regulation of endodeoxyribonuclease activity / signaling adaptor activity / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / negative regulation of Wnt signaling pathway / protein targeting to peroxisome / protein kinase A binding / activation-induced cell death of T cells / positive regulation of mitochondrial depolarization / supercoiled DNA binding / translation regulator activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / phagocytic cup / ion channel inhibitor activity / negative regulation of smoothened signaling pathway / positive regulation of apoptotic signaling pathway / blastocyst development / ribonucleoprotein complex assembly / ubiquitin-like protein conjugating enzyme binding / iron-sulfur cluster binding / positive regulation of cellular component movement / entry of bacterium into host cell / negative regulation of cell-cell adhesion / fibroblast growth factor binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / rescue of stalled ribosome / adherens junction organization / bone development / positive regulation of T cell receptor signaling pathway / poly(U) RNA binding / GTPase activating protein binding / stress granule assembly / DNA-(apurinic or apyrimidinic site) lyase / monocyte chemotaxis / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of ubiquitin-protein transferase activity / BH3 domain binding
Ribosomal protein S27a / Ribosomal protein L25/L23 / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L30, N-terminal / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein S5, N-terminal ...Ribosomal protein S27a / Ribosomal protein L25/L23 / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L30, N-terminal / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein S5, N-terminal / TRASH domain / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / Cadherin prodomain / Ribosomal protein L37ae/L37e / Ribosomal protein S13-like, H2TH / WD40/YVTN repeat-like-containing domain superfamily / KOW / Ribosomal protein S19A/S15e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L13 / Ribosomal protein L24/L26, conserved site / S15/NS1, RNA-binding / Ribosomal protein L7, eukaryotic / Ribosomal protein S12/S23 / Ribosomal protein S30 / Ribosomal protein L41 / Ribosomal protein L34Ae / Translation protein SH3-like domain superfamily / Translation protein, beta-barrel domain superfamily / K homology domain superfamily, prokaryotic type / Cadherin-like superfamily / K homology domain-like, alpha/beta / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / WD40 repeat, conserved site / Ribosomal protein L3, conserved site / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L19/L19e, domain 1 / Ribosomal S24e conserved site / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L10e/L16 / WD40-repeat-containing domain / Ribosomal protein L30, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein S4, conserved site / Ribosomal S11, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein L13e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L27e / Ribosomal protein S26e / Ribosomal protein L11/L12 / 60S ribosomal protein L6E / Ribosomal protein L24e-related / Ribosomal protein L23/L25, conserved site / Ribosomal protein S8e / Ribosomal protein L22/L17 / Ribosomal protein L21e / Ribosomal protein S5 / Ribosomal protein L15, conserved site / Ribosomal protein L10e / Ribosomal protein S14 / Ribosomal protein S17e / Ribosomal protein S19e / Ribosomal protein S3, C-terminal
60S ribosomal protein L24 / 60S ribosomal protein L41 / Ubiquitin-40S ribosomal protein S27a / Ubiquitin-60S ribosomal protein L40 / 60S ribosomal protein L38 / 40S ribosomal protein S21 / Receptor of activated protein C kinase 1 / 60S ribosomal protein L23 / 60S ribosomal protein L36a / 60S ribosomal protein L19 ...60S ribosomal protein L24 / 60S ribosomal protein L41 / Ubiquitin-40S ribosomal protein S27a / Ubiquitin-60S ribosomal protein L40 / 60S ribosomal protein L38 / 40S ribosomal protein S21 / Receptor of activated protein C kinase 1 / 60S ribosomal protein L23 / 60S ribosomal protein L36a / 60S ribosomal protein L19 / 60S ribosomal protein L18a / 60S ribosomal protein L6 / 60S ribosomal protein L18 / 60S ribosomal protein L11 / 60S ribosomal protein L36 / 60S ribosomal protein L8 / 40S ribosomal protein S11 / 60S ribosomal protein L32 / 60S ribosomal protein L9 / 40S ribosomal protein S5 / 40S ribosomal protein S9 / 60S ribosomal protein L28 / 60S ribosomal protein L21 / 60S ribosomal protein L5 / 60S ribosomal protein L27a / 60S ribosomal protein L35 / 40S ribosomal protein S27 / 60S ribosomal protein L13a / 60S ribosomal protein L3 / 40S ribosomal protein S19 / 60S ribosomal protein L4 / 60S ribosomal protein L22 / 60S ribosomal protein L12 / 60S ribosomal protein L29 / 60S ribosomal protein L10 / 60S ribosomal protein L13 / 40S ribosomal protein S12 / 40S ribosomal protein S3 / 40S ribosomal protein S4, Y isoform 1 / 60S ribosomal protein L17 / 60S ribosomal protein L7 / 60S ribosomal protein L35a / 40S ribosomal protein S2 / Cadherin-1 / 40S ribosomal protein SA / 60S acidic ribosomal protein P0 / 40S ribosomal protein S30 / 40S ribosomal protein S10 / 60S ribosomal protein L34 / 60S ribosomal protein L10a / 40S ribosomal protein S13 / 60S ribosomal protein L31 / 60S ribosomal protein L39 / 60S ribosomal protein L30 / 40S ribosomal protein S30 / 40S ribosomal protein S28 / 40S ribosomal protein S26 / 40S ribosomal protein S25 / 40S ribosomal protein S24 / 40S ribosomal protein S15 / 60S ribosomal protein L23 / 40S ribosomal protein S6 / 60S ribosomal protein L23a / 60S ribosomal protein L7a / 40S ribosomal protein S29 / 60S ribosomal protein L14 / 40S ribosomal protein S18 / 40S ribosomal protein S23 / 40S ribosomal protein S14 / 40S ribosomal protein S16 / 40S ribosomal protein S15a / 40S ribosomal protein S8 / 40S ribosomal protein S7 / 60S ribosomal protein L37 / 60S ribosomal protein L37a / 60S ribosomal protein L27 / 60S ribosomal protein L15 / 60S ribosomal protein L26 / 40S ribosomal protein S3a / 40S ribosomal protein S20 / 40S ribosomal protein S17
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi, W. / Cate, J.H.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01-GM065050 United States
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule.
Authors: Wenfei Li / Fred R Ward / Kim F McClure / Stacey Tsai-Lan Chang / Elizabeth Montabana / Spiros Liras / Robert G Dullea / Jamie H D Cate /
Abstract: The drug-like molecule PF-06446846 (PF846) binds the human ribosome and selectively blocks the translation of a small number of proteins by an unknown mechanism. In structures of PF846-stalled human ...The drug-like molecule PF-06446846 (PF846) binds the human ribosome and selectively blocks the translation of a small number of proteins by an unknown mechanism. In structures of PF846-stalled human ribosome nascent chain complexes, PF846 binds in the ribosome exit tunnel in a eukaryotic-specific pocket formed by 28S ribosomal RNA, and alters the path of the nascent polypeptide chain. PF846 arrests the translating ribosome in the rotated state of translocation, in which the peptidyl-transfer RNA 3'-CCA end is improperly docked in the peptidyl transferase center. Selections of messenger RNAs from mRNA libraries using translation extracts reveal that PF846 can stall translation elongation, arrest termination or even enhance translation, depending on nascent chain sequence context. These results illuminate how a small molecule selectively targets translation by the human ribosome, and provides a foundation for developing small molecules that modulate the production of proteins of therapeutic interest.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
AA: 60S ribosomal protein L8
BA: 40S ribosomal protein SA
AB: 60S ribosomal protein L3
BB: 40S ribosomal protein S3a
AC: 60S ribosomal protein L4
BC: 40S ribosomal protein S2
A3: 5.8S ribosomal RNA
A4: 5S ribosomal RNA
AD: 60S ribosomal protein L5
AE: 60S ribosomal protein L6
AF: 60S ribosomal protein L7
AG: 60S ribosomal protein L7a
AH: 60S ribosomal protein L9
AI: 60S ribosomal protein L10
AJ: 60S ribosomal protein L11
AK: 60S acidic ribosomal protein P0
AL: 60S ribosomal protein L13
AM: 60S ribosomal protein L14
AN: 60S ribosomal protein L15
AO: 60S ribosomal protein L13a
AP: 60S ribosomal protein L17
AQ: 60S ribosomal protein L18
AR: 60S ribosomal protein L19
AS: 60S ribosomal protein L18a
AT: 60S ribosomal protein L21
AU: 60S ribosomal protein L22
AV: 60S ribosomal protein L23
AW: 60S ribosomal protein L24
AX: 60S ribosomal protein L23a
AY: 60S ribosomal protein L26
AZ: 60S ribosomal protein L27
Aa: 60S ribosomal protein L27a
Ab: 60S ribosomal protein L29
Ac: 60S ribosomal protein L30
Ad: 60S ribosomal protein L31
Ae: 60S ribosomal protein L32
Af: 60S ribosomal protein L35a
Ag: 60S ribosomal protein L34
Ah: 60S ribosomal protein L35
Ai: 60S ribosomal protein L36
Aj: 60S ribosomal protein L37
Ak: 60S ribosomal protein L38
Al: 60S ribosomal protein L39
Am: 60S ribosomal protein L40
An: 60S ribosomal protein L41
Ao: 60S ribosomal protein L36a
Ap: 60S ribosomal protein L37a
Aq: 60S ribosomal protein L12
At: 60S ribosomal protein L28
Au: 60S ribosomal protein L10a
A2: 28S ribosomal RNA
B1: 18S ribosomal RNA
BD: 40S ribosomal protein S3
BE: 40S ribosomal protein S4, Y isoform 1
BF: 40S ribosomal protein S5
BG: 40S ribosomal protein S6
BH: 40S ribosomal protein S7
BI: 40S ribosomal protein S8
BJ: 40S ribosomal protein S9
BK: 40S ribosomal protein S10
BL: 40S ribosomal protein S11
BM: 40S ribosomal protein S12
BN: 40S ribosomal protein S13
BO: 40S ribosomal protein S14
BP: 40S ribosomal protein S15
BQ: 40S ribosomal protein S16
BR: 40S ribosomal protein S17
BS: 40S ribosomal protein S18
BT: 40S ribosomal protein S19
BU: 40S ribosomal protein S20
BV: 40S ribosomal protein S21
BW: 40S ribosomal protein S15a
BX: 40S ribosomal protein S23
BY: 40S ribosomal protein S24
BZ: 40S ribosomal protein S25
Ba: 40S ribosomal protein S26
Bb: 40S ribosomal protein S27
Bc: 40S ribosomal protein S28
Bd: 40S ribosomal protein S29
Be: 40S ribosomal protein S30
Bf: 40S ribosomal protein S27a
Bg: Receptor of activated protein C kinase 1
Bv: tRNA
Bx: mRNA
A: Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,206,720417
Polymers3,198,03685
Non-polymers8,684332
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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60S ribosomal protein ... , 44 types, 44 molecules AAABACADAEAFAGAHAIAJALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAdAe...

#1: Protein 60S ribosomal protein L8 / / Large ribosomal subunit protein uL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62917
#3: Protein 60S ribosomal protein L3 / / HIV-1 TAR RNA-binding protein B / TARBP-B / Large ribosomal subunit protein uL3


Mass: 45222.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39023
#5: Protein 60S ribosomal protein L4 / / 60S ribosomal protein L1 / Large ribosomal subunit protein uL4


Mass: 41171.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36578
#9: Protein 60S ribosomal protein L5 / / Large ribosomal subunit protein uL18


Mass: 34091.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46777
#10: Protein 60S ribosomal protein L6 / / Large ribosomal subunit protein eL6 / Neoplasm-related protein C140 / Tax-responsive enhancer ...Large ribosomal subunit protein eL6 / Neoplasm-related protein C140 / Tax-responsive enhancer element-binding protein 107 / TaxREB107


Mass: 22262.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02878
#11: Protein 60S ribosomal protein L7 / / Large ribosomal subunit protein uL30


Mass: 27733.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18124
#12: Protein 60S ribosomal protein L7a / / Large ribosomal subunit protein eL8 / PLA-X polypeptide / Surfeit locus protein 3


Mass: 26724.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62424
#13: Protein 60S ribosomal protein L9 / / Large ribosomal subunit protein uL6


Mass: 21770.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32969
#14: Protein 60S ribosomal protein L10 / / Laminin receptor homolog / Large ribosomal subunit protein uL16 / Protein QM / Ribosomal protein ...Laminin receptor homolog / Large ribosomal subunit protein uL16 / Protein QM / Ribosomal protein L10 / Tumor suppressor QM


Mass: 24381.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27635
#15: Protein 60S ribosomal protein L11 / / CLL-associated antigen KW-12 / Large ribosomal subunit protein uL5


Mass: 19270.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62913
#17: Protein 60S ribosomal protein L13 / / Breast basic conserved protein 1 / Large ribosomal subunit protein eL13


Mass: 23574.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P26373
#18: Protein 60S ribosomal protein L14 / / CAG-ISL 7 / Large ribosomal subunit protein eL14


Mass: 16220.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50914
#19: Protein 60S ribosomal protein L15 / / Large ribosomal subunit protein eL15


Mass: 24076.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61313
#20: Protein 60S ribosomal protein L13a / / 23 kDa highly basic protein / Large ribosomal subunit protein uL13


Mass: 22820.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40429
#21: Protein 60S ribosomal protein L17 / / 60S ribosomal protein L23 / Large ribosomal subunit protein uL22 / PD-1


Mass: 17757.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18621
#22: Protein 60S ribosomal protein L18 / / Large ribosomal subunit protein eL18


Mass: 21556.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07020
#23: Protein 60S ribosomal protein L19 / / Large ribosomal subunit protein eL19


Mass: 21742.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P84098
#24: Protein 60S ribosomal protein L18a / / Large ribosomal subunit protein eL20


Mass: 20661.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q02543
#25: Protein 60S ribosomal protein L21 / / Large ribosomal subunit protein eL21


Mass: 18276.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46778
#26: Protein 60S ribosomal protein L22 / / EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding ...EBER-associated protein / EAP / Epstein-Barr virus small RNA-associated protein / Heparin-binding protein HBp15 / Large ribosomal subunit protein eL22


Mass: 11481.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35268
#27: Protein 60S ribosomal protein L23 /


Mass: 13828.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BTQ7, UniProt: P62829*PLUS
#28: Protein 60S ribosomal protein L24 / / 60S ribosomal protein L30 / Large ribosomal subunit protein eL24


Mass: 14087.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83731
#29: Protein 60S ribosomal protein L23a / / Large ribosomal subunit protein uL23


Mass: 13614.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62750
#30: Protein 60S ribosomal protein L26 / / Large ribosomal subunit protein uL24


Mass: 15161.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61254
#31: Protein 60S ribosomal protein L27 / / Large ribosomal subunit protein eL27


Mass: 15647.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61353
#32: Protein 60S ribosomal protein L27a / / Large ribosomal subunit protein uL15


Mass: 16473.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46776
#33: Protein 60S ribosomal protein L29 / / Cell surface heparin-binding protein HIP / Large ribosomal subunit protein eL29


Mass: 13965.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P47914
#34: Protein 60S ribosomal protein L30 / / Large ribosomal subunit protein eL30


Mass: 11500.556 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62888
#35: Protein 60S ribosomal protein L31 / / Large ribosomal subunit protein eL31


Mass: 12506.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62899
#36: Protein 60S ribosomal protein L32 / / Large ribosomal subunit protein eL32


Mass: 15179.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62910
#37: Protein 60S ribosomal protein L35a / / Cell growth-inhibiting gene 33 protein / Large ribosomal subunit protein eL33


Mass: 12433.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18077
#38: Protein 60S ribosomal protein L34 / / Large ribosomal subunit protein eL34


Mass: 12994.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49207
#39: Protein 60S ribosomal protein L35 / / Large ribosomal subunit protein uL29


Mass: 14462.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42766
#40: Protein 60S ribosomal protein L36 / / Large ribosomal subunit protein eL36


Mass: 11373.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3U8
#41: Protein 60S ribosomal protein L37 / / G1.16 / Large ribosomal subunit protein eL37


Mass: 9864.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61927
#42: Protein 60S ribosomal protein L38 / / Large ribosomal subunit protein eL38


Mass: 8107.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63173
#43: Protein/peptide 60S ribosomal protein L39 / / Large ribosomal subunit protein eL39


Mass: 6295.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62891
#44: Protein/peptide 60S ribosomal protein L40 / / CEP52 / Ubiquitin A-52 residue ribosomal protein fusion product 1


Mass: 5957.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62987
#45: Protein/peptide 60S ribosomal protein L41 / / HG12 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945
#46: Protein 60S ribosomal protein L36a / / 60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 ...60S ribosomal protein L44 / Cell growth-inhibiting gene 15 protein / Cell migration-inducing gene 6 protein / Large ribosomal subunit protein eL42


Mass: 12345.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83881
#47: Protein 60S ribosomal protein L37a / / Large ribosomal subunit protein eL43


Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61513
#48: Protein 60S ribosomal protein L12 / / Large ribosomal subunit protein uL11


Mass: 14942.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30050
#49: Protein 60S ribosomal protein L28 / / Large ribosomal subunit protein eL28


Mass: 13991.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46779
#50: Protein 60S ribosomal protein L10a / / CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down- ...CSA-19 / Large ribosomal subunit protein uL1 / Neural precursor cell expressed developmentally down-regulated protein 6 / NEDD-6


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62906

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40S ribosomal protein ... , 32 types, 32 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBdBeBf

#2: Protein 40S ribosomal protein SA / / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 24245.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#4: Protein 40S ribosomal protein S3a / / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 24660.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#6: Protein 40S ribosomal protein S2 / / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 24574.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#53: Protein 40S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 24357.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#54: Protein 40S ribosomal protein S4, Y isoform 1 / Ribosome / Small ribosomal subunit protein eS4


Mass: 28893.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P22090
#55: Protein 40S ribosomal protein S5 / / Small ribosomal subunit protein uS7


Mass: 21424.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#56: Protein 40S ribosomal protein S6 / / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 26913.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#57: Protein 40S ribosomal protein S7 / / Small ribosomal subunit protein eS7


Mass: 20990.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#58: Protein 40S ribosomal protein S8 / / Small ribosomal subunit protein eS8


Mass: 24132.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#59: Protein 40S ribosomal protein S9 / / Small ribosomal subunit protein uS4


Mass: 21222.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#60: Protein 40S ribosomal protein S10 / / Small ribosomal subunit protein eS10


Mass: 11773.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#61: Protein 40S ribosomal protein S11 / / Small ribosomal subunit protein uS17


Mass: 17910.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#62: Protein 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 13393.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#63: Protein 40S ribosomal protein S13 / / Small ribosomal subunit protein uS15


Mass: 17057.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#64: Protein 40S ribosomal protein S14 / / Small ribosomal subunit protein uS11


Mass: 14544.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#65: Protein 40S ribosomal protein S15 / / RIG protein / Small ribosomal subunit protein uS19


Mass: 14273.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#66: Protein 40S ribosomal protein S16 / / Small ribosomal subunit protein uS9


Mass: 15765.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#67: Protein 40S ribosomal protein S17 / / Small ribosomal subunit protein eS17


Mass: 14447.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#68: Protein 40S ribosomal protein S18 / / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 16383.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#69: Protein 40S ribosomal protein S19 / / Small ribosomal subunit protein eS19


Mass: 15822.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#70: Protein 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 11029.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#71: Protein 40S ribosomal protein S21 / / Small ribosomal subunit protein eS21


Mass: 8863.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#72: Protein 40S ribosomal protein S15a / / Small ribosomal subunit protein uS8


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#73: Protein 40S ribosomal protein S23 / / Small ribosomal subunit protein uS12


Mass: 15372.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#74: Protein 40S ribosomal protein S24 / / Small ribosomal subunit protein eS24


Mass: 14489.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#75: Protein 40S ribosomal protein S25 / / Small ribosomal subunit protein eS25


Mass: 9801.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#76: Protein 40S ribosomal protein S26 / / Small ribosomal subunit protein eS26


Mass: 11087.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#77: Protein 40S ribosomal protein S27 / / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9000.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#78: Protein 40S ribosomal protein S28 / / Small ribosomal subunit protein eS28


Mass: 7007.069 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#79: Protein 40S ribosomal protein S29 / / Small ribosomal subunit protein uS14


Mass: 6121.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#80: Protein 40S ribosomal protein S30 /


Mass: 6239.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: E9PR30, UniProt: P62861*PLUS
#81: Protein 40S ribosomal protein S27a / Ribosome / Ubiquitin carboxyl extension protein 80


Mass: 8645.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979

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RNA chain , 6 types, 6 molecules A3A4A2B1BvBx

#7: RNA chain 5.8S ribosomal RNA /


Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#8: RNA chain 5S ribosomal RNA /


Mass: 38385.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#51: RNA chain 28S ribosomal RNA /


Mass: 1170164.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#52: RNA chain 18S ribosomal RNA /


Mass: 551108.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#83: RNA chain tRNA / Transfer RNA


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#84: RNA chain mRNA / Messenger RNA


Mass: 4853.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Protein , 2 types, 2 molecules AKBg

#16: Protein 60S acidic ribosomal protein P0 / 60S ribosomal protein L10E / Large ribosomal subunit protein uL10


Mass: 12505.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05388
#82: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 34726.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244

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Protein/peptide , 1 types, 1 molecules A

#85: Protein/peptide Cadherin-1 / / CAM 120/80 / Epithelial cadherin / E-cadherin / Uvomorulin


Mass: 4040.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P12830

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Non-polymers , 3 types, 332 molecules

#86: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 326 / Source method: obtained synthetically / Formula: Mg
#87: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#88: Chemical ChemComp-MVM / N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide


Mass: 433.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20ClN7O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA)
Type: RIBOSOME / Entity ID: #1-#85 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16594 / Symmetry type: POINT

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