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- PDB-6hcf: Structure of the rabbit 80S ribosome stalled on globin mRNA at th... -

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Basic information

Entry
Database: PDB / ID: 6hcf
TitleStructure of the rabbit 80S ribosome stalled on globin mRNA at the stop codon
Components
  • (40S ribosomal protein ...) x 6
  • (60S ribosomal protein ...) x 5
  • (Ribosomal protein ...) x 15
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • ATP binding cassette subfamily E member 1
  • P-site tRNA
  • RACK1Receptor for activated C kinase 1
  • eL13
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL24
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL38
  • eL39
  • eL40
  • eL41
  • eL42
  • eL43
  • eL8
  • eRF1(AAQ)
  • eS10
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS4
  • eS8
  • mRNAMessenger RNA
  • nascent chain
  • uL1
  • uL10
  • uL13
  • uL15
  • uL22
  • uL23
  • uL29
  • uL3
  • uL30
  • uL4
  • uL6
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS19
  • uS2
  • uS3
  • uS5
KeywordsRIBOSOME / Translation / Quality Control
Function / homology
Function and homology information


regulation of translation involved in cellular response to UV / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA N-glycosylase activity / response to TNF agonist / positive regulation of base-excision repair / negative regulation of DNA repair / oxidized pyrimidine DNA binding / 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 ...regulation of translation involved in cellular response to UV / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA N-glycosylase activity / response to TNF agonist / positive regulation of base-excision repair / negative regulation of DNA repair / oxidized pyrimidine DNA binding / 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 / mammalian oogenesis stage / NF-kappaB complex / cytosolic ribosome / positive regulation of endodeoxyribonuclease activity / oxidized purine DNA binding / protein kinase A binding / activation-induced cell death of T cells / supercoiled DNA binding / ubiquitin-like protein conjugating enzyme binding / positive regulation of T cell receptor signaling pathway / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of activated T cell proliferation / erythrocyte development / TOR signaling / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / spindle assembly / ribosomal large subunit biogenesis / positive regulation of JUN kinase activity / ribosomal small subunit biogenesis / gastrulation / positive regulation of microtubule polymerization / polysome / cellular response to leukemia inhibitory factor / Hsp70 protein binding / polysomal ribosome / negative regulation of protein ubiquitination / endodeoxyribonuclease activity / positive regulation of interleukin-2 production / rough endoplasmic reticulum / positive regulation of translation / mitotic spindle / ruffle membrane / Hsp90 protein binding / chromosome segregation / small ribosomal subunit rRNA binding / cytoplasmic ribonucleoprotein granule / DNA damage response, detection of DNA damage / mRNA 5'-UTR binding / cellular response to gamma radiation / placenta development / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / G1/S transition of mitotic cell cycle / rRNA processing / cellular response to hydrogen peroxide / positive regulation of NIK/NF-kappaB signaling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / cell body / 5S rRNA binding / cellular response to tumor necrosis factor / cytosolic small ribosomal subunit / glucose homeostasis / small ribosomal subunit / T cell differentiation in thymus / mitochondrial inner membrane / microtubule binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / postsynaptic density / positive regulation of NF-kappaB transcription factor activity / mitochondrial matrix / cell differentiation / translation / ATPase / cell division / mRNA binding / transcription factor binding / positive regulation of apoptotic process / dendrite / apoptotic process / protein-containing complex binding / nucleolus / positive regulation of cell population proliferation / protein kinase binding / negative regulation of apoptotic process / Golgi apparatus / perinuclear region of cytoplasm / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus
Ribosomal L28e protein family / G-protein beta WD-40 repeat / Ribosomal protein L15e, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L39e, conserved site ...Ribosomal L28e protein family / G-protein beta WD-40 repeat / Ribosomal protein L15e, conserved site / Ribosomal protein L11, conserved site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, C-terminal / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L39e, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L23 / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin domain / Ubiquitin conserved site / Ribosomal protein L3, conserved site / Ribosomal protein L5, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S6e, conserved site / Ribosomal protein L1, conserved site / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L39e domain superfamily / Ribosomal protein L2, C-terminal / Ribosomal protein L31e domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein L24e, conserved site / in:ipr023106: / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / WD40 repeat, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S17, archaeal/eukaryotic / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S6, eukaryotic / RLI1 / Ribosomal protein L25/L23 / Ribosomal protein L30, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S13/S15, N-terminal / WD40/YVTN repeat-like-containing domain superfamily / Nucleic acid-binding, OB-fold / Zinc-binding ribosomal protein / Ribosomal protein L37ae/L37e / TRASH domain / Ribosomal protein S13-like, H2TH / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Translation protein, beta-barrel domain superfamily / Ribosomal protein L2, domain 3 / K homology domain-like, alpha/beta / Ribosomal protein S3, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / ABC transporter, conserved site / Ribosomal protein L10e/L16 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein L1/ribosomal biogenesis protein / RNase L inhibitor RLI-like, possible metal-binding domain / Plectin/S10 domain / Ribosomal protein S9/S16 / Ribosomal protein S15 / Ribosomal L15 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein L14 / Ribosomal_S17 N-terminal / Ribosomal protein S17 / S4 domain / Ribosomal protein S13/S18 / Ribosomal protein S4/S9 N-terminal domain / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L16p/L10e
40S ribosomal protein S27 / Ribosomal protein L37 / 40S ribosomal protein S29 / 60S ribosomal protein L28 / Ribosomal protein L32 / 40S ribosomal protein S15 / 40S ribosomal protein S15a / 60S ribosomal protein L27 / 60S ribosomal protein L21 / Ribosomal protein L26 ...40S ribosomal protein S27 / Ribosomal protein L37 / 40S ribosomal protein S29 / 60S ribosomal protein L28 / Ribosomal protein L32 / 40S ribosomal protein S15 / 40S ribosomal protein S15a / 60S ribosomal protein L27 / 60S ribosomal protein L21 / Ribosomal protein L26 / 40S ribosomal protein S13 / 60S ribosomal protein L12 / Ribosomal protein / 60S ribosomal protein L6 / 40S ribosomal protein S27a / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S20 / 60S ribosomal protein L35 / 60S ribosomal protein L31 / 40S ribosomal protein S7 / Uncharacterized protein / 60S ribosomal protein L29 / Uncharacterized protein / 40S ribosomal protein S12 / 60S ribosomal protein L35a / Ribosomal_L23eN domain-containing protein / Ribosomal protein L24 / 40S ribosomal protein S9 / Ribosomal protein L10 / 40S ribosomal protein S3a / 60S ribosomal protein L9 / 60S ribosomal protein L9 / 40S ribosomal protein S18 / 60S ribosomal protein L17 / 60S ribosomal protein L11 / Uncharacterized protein / 40S ribosomal protein S17 / 60S ribosomal protein L36 / Uncharacterized protein / 60S ribosomal protein L8 / 40S ribosomal protein S11 / S10_plectin domain-containing protein / 40S ribosomal protein S3 / Uncharacterized protein / 40S ribosomal protein S6 / Ribosomal protein L3 / 40S ribosomal protein S28 / Ribosomal protein S5 / 60S ribosomal protein L30 / 40S ribosomal protein S30 / 60S ribosomal protein L23 / Ribosomal protein L15 / 60S ribosomal protein L14 / Ribosomal_L18_c domain-containing protein / 40S ribosomal protein S25
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsJuszkiewicz, S. / Chandrasekaran, V. / Lin, Z. / Kraatz, S. / Ramakrishnan, V. / Hegde, R.S.
Funding support United Kingdom, France, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_A022_1007 United Kingdom
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
Louis-Jeantet Foundation France
CitationJournal: Mol Cell / Year: 2018
Title: ZNF598 Is a Quality Control Sensor of Collided Ribosomes.
Authors: Szymon Juszkiewicz / Viswanathan Chandrasekaran / Zhewang Lin / Sebastian Kraatz / V Ramakrishnan / Ramanujan S Hegde /
Abstract: Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates ...Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates stalled ribosomes selectively is unclear. Here, we find that the minimal unit engaged by ZNF598 is the collided di-ribosome, a molecular species that arises when a trailing ribosome encounters a slower leading ribosome. The collided di-ribosome structure reveals an extensive 40S-40S interface in which the ubiquitination targets of ZNF598 reside. The paucity of 60S interactions allows for different ribosome rotation states, explaining why ZNF598 recognition is indifferent to how the leading ribosome has stalled. The use of ribosome collisions as a proxy for stalling allows the degree of tolerable slowdown to be tuned by the initiation rate on that mRNA; hence, the threshold for triggering quality control is substrate specific. These findings illustrate how higher-order ribosome architecture can be exploited by cellular factors to monitor translation status.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Experimental preparation
Category: atom_site / em_admin ...atom_site / em_admin / em_sample_support / pdbx_data_processing_status / pdbx_database_proc / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_auth_asym_id / _atom_site.pdbx_auth_atom_name / _atom_site.pdbx_auth_comp_id / _atom_site.pdbx_auth_seq_id / _atom_site.type_symbol / _em_admin.last_update / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id / _struct_asym.pdbx_PDB_id / _struct_asym.pdbx_alt_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id

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Structure visualization

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Assembly

Deposited unit
A1: 18S ribosomal RNA
B1: uS2
C1: 40S ribosomal protein S3a
D1: uS5
E1: uS3
F1: eS4
G1: Ribosomal protein S5
H1: 40S ribosomal protein S6
I1: 40S ribosomal protein S7
J1: eS8
K1: Ribosomal protein S9 (Predicted)
L1: eS10
M1: Ribosomal protein S11
N1: 40S ribosomal protein S12
O1: uS15
P1: uS11
Q1: uS19
R1: Ribosomal protein S16
S1: eS17
T1: uS13
U1: eS19
V1: uS10
W1: eS21
X1: Ribosomal protein S15a
Y1: uS12
Z1: eS24
a1: eS25
b1: eS26
c1: 40S ribosomal protein S27
d1: Ribosomal protein S28
e1: uS14
f1: 40S ribosomal protein S30
g1: Ribosomal protein S27a
h1: RACK1
j1: eRF1(AAQ)
k1: ATP binding cassette subfamily E member 1
52: 28S ribosomal RNA
72: 5S ribosomal RNA
82: 5.8S ribosomal RNA
A3: Ribosomal protein L8
B3: uL3
C3: uL4
E3: 60S ribosomal protein L6
F3: uL30
H3: uL6
L3: eL13
M3: Ribosomal protein L14
N3: Ribosomal protein L15
O3: uL13
P3: uL22
Q3: eL18
R3: eL19
S3: eL20
T3: eL21
U3: eL22
V3: Ribosomal protein L23
W3: eL24
X3: uL23
Y3: Ribosomal protein L26
Z3: 60S ribosomal protein L27
a3: uL15
b3: eL29
c3: eL30
d3: eL31
e3: eL32
f3: eL33
g3: eL34
h3: uL29
i3: 60S ribosomal protein L36
j3: Ribosomal protein L37
k3: eL38
l3: eL39
m3: eL40
n3: eL41
o3: eL42
p3: eL43
r3: eL28
s3: uL10
t3: Ribosomal protein L12
23: P-site tRNA
w3: mRNA
J3: Ribosomal protein L11
G3: eL8
D3: 60S ribosomal protein L5
I3: 60S ribosomal protein L10
1: nascent chain
u3: uL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,572,568397
Polymers3,564,05087
Non-polymers8,518310
Water724
1


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

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Components

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RNA chain , 6 types, 6 molecules A152728223w3

#1: RNA chain 18S ribosomal RNA /


Mass: 602778.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#37: RNA chain 28S ribosomal RNA /


Mass: 1177577.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#38: RNA chain 5S ribosomal RNA /


Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#39: RNA chain 5.8S ribosomal RNA /


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#80: RNA chain P-site tRNA


Mass: 24436.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#81: RNA chain mRNA / Messenger RNA


Mass: 7387.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Protein , 53 types, 53 molecules B1D1E1F1J1L1O1P1Q1S1T1U1V1W1Y1Z1a1b1e1h1j1k1B3C3F3H3L3O3P3Q3...

#2: Protein uS2


Mass: 32958.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#4: Protein uS5


Mass: 31327.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: Protein uS3


Mass: 26715.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#6: Protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#10: Protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#12: Protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#15: Protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#16: Protein uS11


Mass: 18133.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#17: Protein uS19


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#19: Protein eS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#20: Protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#21: Protein eS19


Mass: 16106.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#22: Protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#23: Protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#25: Protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#26: Protein eS24


Mass: 15107.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#27: Protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#28: Protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#31: Protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#34: Protein RACK1 / Receptor for activated C kinase 1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#35: Protein eRF1(AAQ)


Mass: 49264.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#36: Protein ATP binding cassette subfamily E member 1


Mass: 67405.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SG72
#41: Protein uL3


Mass: 46107.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#42: Protein uL4


Mass: 47727.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#44: Protein uL30


Mass: 29201.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB1
#45: Protein uL6


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TX33, UniProt: G1SWI6*PLUS
#46: Protein eL13


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#49: Protein uL13


Mass: 23533.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: Protein uL22


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TVT6
#51: Protein eL18


Mass: 21699.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#52: Protein eL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: Protein eL20


Mass: 20827.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#54: Protein eL21 /


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#55: Protein eL22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#57: Protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#58: Protein uL23


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#61: Protein uL15


Mass: 16620.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#62: Protein eL29


Mass: 24931.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#63: Protein eL30


Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#64: Protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#65: Protein eL32 / CD59


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#66: Protein eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#67: Protein eL34 /


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#68: Protein uL29


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#71: Protein eL38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#72: Protein eL39


Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#73: Protein eL40


Mass: 11699.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#76: Protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#77: Protein eL28


Mass: 15783.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#78: Protein uL10


Mass: 34380.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#83: Protein eL8


Mass: 36221.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#87: Protein uL1


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8

+
40S ribosomal protein ... , 6 types, 6 molecules C1H1I1N1c1f1

#3: Protein 40S ribosomal protein S3a /


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#8: Protein 40S ribosomal protein S6 /


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#9: Protein 40S ribosomal protein S7 /


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#14: Protein 40S ribosomal protein S12 /


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#29: Protein 40S ribosomal protein S27 /


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#32: Protein 40S ribosomal protein S30 /


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2

+
Ribosomal protein ... , 15 types, 15 molecules G1K1M1R1X1d1g1A3M3N3V3Y3j3t3J3

#7: Protein Ribosomal protein S5 /


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#11: Protein Ribosomal protein S9 (Predicted) / Ribosome


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#13: Protein Ribosomal protein S11 /


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#18: Protein Ribosomal protein S16 /


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#24: Protein Ribosomal protein S15a / Ribosome


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#30: Protein Ribosomal protein S28 /


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#33: Protein Ribosomal protein S27a / Ribosome


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#40: Protein Ribosomal protein L8 /


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#47: Protein Ribosomal protein L14 /


Mass: 23870.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ12
#48: Protein Ribosomal protein L15 /


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#56: Protein Ribosomal protein L23 /


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#59: Protein Ribosomal protein L26 /


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#70: Protein Ribosomal protein L37 /


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#79: Protein Ribosomal protein L12 /


Mass: 17847.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMR7
#82: Protein Ribosomal protein L11 /


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8

+
60S ribosomal protein ... , 5 types, 5 molecules E3Z3i3D3I3

#43: Protein 60S ribosomal protein L6 /


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#60: Protein 60S ribosomal protein L27 /


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#69: Protein 60S ribosomal protein L36 /


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#84: Protein 60S ribosomal protein L5 /


Mass: 34481.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#85: Protein 60S ribosomal protein L10 / / Ribosomal protein L10 (Predicted)


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2

+
Protein/peptide , 2 types, 2 molecules n31

#74: Protein/peptide eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#86: Protein/peptide nascent chain


Mass: 1581.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

+
Non-polymers , 4 types, 314 molecules

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


Mass: 24.305 Da / Num. of mol.: 300 / Source method: obtained synthetically / Formula: Mg
#89: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#90: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#91: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Rabbit 80S ribosome stalled on globin mRNA at the stop codonRIBOSOME#1-#870MULTIPLE SOURCES
2RibosomeRIBOSOME#1-#34, #36-#871NATURAL
3RACK1Receptor for activated C kinase 1COMPLEX#351RECOMBINANT
Molecular weightValue: 4.3 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Oryctolagus cuniculus (rabbit)9986
33Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 1.79 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71954 / Symmetry type: POINT

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