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- PDB-6zvj: Structure of a human ABCE1-bound 43S pre-initiation complex - State II -

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Entry
Database: PDB / ID: 6zvj
TitleStructure of a human ABCE1-bound 43S pre-initiation complex - State II
Components
  • (40S ribosomal protein ...) x 31
  • (Eukaryotic translation initiation factor 3 subunit ...) x 12
  • 18S ribosomal RNA
  • 60S ribosomal protein L41
  • ATP-binding cassette sub-family E member 1
  • Eukaryotic translation initiation factor 1
  • RNA recognition motif (unknown)
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
KeywordsRIBOSOME / Translation / Initiation / Ribosome Recycling / ABC Proteins
Function / homology
Function and homology information


cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / positive regulation of mRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / mRNA cap binding / IRES-dependent viral translational initiation / deubiquitinase activity / translation factor activity, RNA binding ...cap-dependent translational initiation / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / positive regulation of mRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / mRNA cap binding / IRES-dependent viral translational initiation / deubiquitinase activity / translation factor activity, RNA binding / multi-eIF complex / eukaryotic translation initiation factor 3 complex / cytoplasmic translational initiation / eukaryotic 43S preinitiation complex / 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 / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / ubiquitin ligase inhibitor activity / laminin receptor activity / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of cell division / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of hydrogen peroxide-induced neuron death / negative regulation of DNA repair / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / response to TNF agonist / oxidized pyrimidine DNA binding / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of ubiquitin protein ligase activity / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of ceramide biosynthetic process / erythrocyte homeostasis / regulation of translational initiation / mammalian oogenesis stage / NF-kappaB complex / negative regulation of phagocytosis / regulation of establishment of cell polarity / ribosomal subunit export from nucleus / positive regulation of endodeoxyribonuclease activity / signaling adaptor activity / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of Wnt signaling pathway / oxidized purine DNA binding / protein targeting to peroxisome / protein kinase A binding / activation-induced cell death of T cells / supercoiled DNA binding / positive regulation of mitochondrial depolarization / 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 / ubiquitin-like protein conjugating enzyme binding / iron-sulfur cluster binding / positive regulation of cellular component movement / fibroblast growth factor binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / rescue of stalled ribosome / positive regulation of T cell receptor signaling pathway / poly(U) RNA 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 / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of activated T cell proliferation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / erythrocyte development / GABA-ergic synapse / regulation of type I interferon-mediated signaling pathway / positive regulation of cyclic-nucleotide phosphodiesterase activity / TOR signaling / ribosomal small subunit export from nucleus / ribosomal small subunit binding / regulation of tumor necrosis factor-mediated signaling pathway / maturation of SSU-rRNA / regulation of translational fidelity / endoribonuclease inhibitor activity / negative regulation of protein kinase B signaling / negative regulation of respiratory burst involved in inflammatory response / T cell proliferation involved in immune response / spindle assembly / negative regulation of ubiquitin-dependent protein catabolic process / small-subunit processome / negative regulation of endoribonuclease activity / positive regulation of JUN kinase activity / SRP-dependent cotranslational protein targeting to membrane
Eukaryotic translation initiation factor SUI1 / Ribosomal protein S17, conserved site / Ribosomal protein S15P / Ribosomal protein S4/S9 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat ...Eukaryotic translation initiation factor SUI1 / Ribosomal protein S17, conserved site / Ribosomal protein S15P / Ribosomal protein S4/S9 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ubiquitin domain / Ribosomal protein S19/S15, superfamily / Ubiquitin conserved site / WD40 repeat, conserved site / Translation initiation factor 3 complex subunit L / Eukaryotic translation initiation factor 3 subunit E, N-terminal / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3, conserved site / Eukaryotic translation initiation factor 3-like domain superfamily / Ribosomal protein S30 / Ribosomal protein S21e, conserved site / RNA recognition motif domain / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit C / JAB1/MPN/MOV34 metalloenzyme domain / Ribosomal protein S7e / Eukaryotic translation initiation factor 3 subunit A / Ribosomal protein S12e / 40S ribosomal protein SA / 40S ribosomal protein S1/3, eukaryotes / Eukaryotic translation initiation factor 3 subunit E / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S28e / Ribosomal protein S17/S11 / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S5/S7 / P-loop containing nucleoside triphosphate hydrolase / Rpn11/EIF3F, C-terminal / Ribosomal protein S7 domain / RNase L inhibitor RLI-like, possible metal-binding domain / Ribosomal protein S19e, conserved site / Ribosomal protein S27 / Ribosomal protein L2, domain 2 / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Eukaryotic translation initiation factor 3 subunit J / Ribosomal protein S12/S23 / Translation initiation factor, beta propellor-like domain / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal S24e conserved site / Ribosomal protein S2, conserved site / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / Ribosomal protein S4, conserved site / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Armadillo-type fold / WD40-repeat-containing domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Ribosomal S11, conserved site / RLI1 / Ribosomal protein S17e, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S14, conserved site / Eukaryotic translation initiation factor 3 subunit D / Ribosomal protein L41 / Ribosomal protein S13, conserved site / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / K homology domain superfamily, prokaryotic type / S15/NS1, RNA-binding / Ribosomal protein S10, conserved site / Eukaryotic translation initiation factor 3 subunit K / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S13-like, H2TH / Zinc-binding ribosomal protein / Eukaryotic translation initiation factor 3 subunit B / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein S15 / Ribosomal protein S2, eukaryotic / Eukaryotic translation initiation factor 3 subunit I / Ribosomal protein S21e / Ribosomal protein S24e / Ribosomal protein S11 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / S27a-like superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S26e superfamily / SUI1 domain / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S27a
40S ribosomal protein S25 / 40S ribosomal protein S16 / 40S ribosomal protein S23 / 40S ribosomal protein S18 / 40S ribosomal protein S29 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S15 ...40S ribosomal protein S25 / 40S ribosomal protein S16 / 40S ribosomal protein S23 / 40S ribosomal protein S18 / 40S ribosomal protein S29 / 40S ribosomal protein S13 / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S15 / 40S ribosomal protein S26 / 40S ribosomal protein S8 / 40S ribosomal protein S28 / 40S ribosomal protein S30 / 60S ribosomal protein L41 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S21 / Receptor of activated protein C kinase 1 / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit K / 40S ribosomal protein S15a / 40S ribosomal protein S7 / 40S ribosomal protein S14 / 40S ribosomal protein S3 / Eukaryotic translation initiation factor 3 subunit C / 40S ribosomal protein S24 / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit J / 40S ribosomal protein S17 / 40S ribosomal protein SA / 40S ribosomal protein S2 / 40S ribosomal protein S12 / 40S ribosomal protein S3a / 40S ribosomal protein S19 / Eukaryotic translation initiation factor 1 / 40S ribosomal protein S27 / 40S ribosomal protein S9 / 40S ribosomal protein S5 / 40S ribosomal protein S10 / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit E / 40S ribosomal protein S20 / ATP-binding cassette sub-family E member 1 / Eukaryotic translation initiation factor 3 subunit L
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsKratzat, H. / Mackens-Kiani, T. / Ameismeier, A. / Cheng, J. / Berninghausen, O. / Becker, T. / Beckmann, R.
Funding support Germany, France, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: EMBO J / Year: 2021
Title: A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes.
Authors: Hanna Kratzat / Timur Mackens-Kiani / Michael Ameismeier / Mia Potocnjak / Jingdong Cheng / Estelle Dacheux / Abdelkader Namane / Otto Berninghausen / Franz Herzog / Micheline Fromont-Racine ...Authors: Hanna Kratzat / Timur Mackens-Kiani / Michael Ameismeier / Mia Potocnjak / Jingdong Cheng / Estelle Dacheux / Abdelkader Namane / Otto Berninghausen / Franz Herzog / Micheline Fromont-Racine / Thomas Becker / Roland Beckmann /
Abstract: In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub-complexes. ...In eukaryotic translation, termination and ribosome recycling phases are linked to subsequent initiation of a new round of translation by persistence of several factors at ribosomal sub-complexes. These comprise/include the large eIF3 complex, eIF3j (Hcr1 in yeast) and the ATP-binding cassette protein ABCE1 (Rli1 in yeast). The ATPase is mainly active as a recycling factor, but it can remain bound to the dissociated 40S subunit until formation of the next 43S pre-initiation complexes. However, its functional role and native architectural context remains largely enigmatic. Here, we present an architectural inventory of native yeast and human ABCE1-containing pre-initiation complexes by cryo-EM. We found that ABCE1 was mostly associated with early 43S, but also with later 48S phases of initiation. It adopted a novel hybrid conformation of its nucleotide-binding domains, while interacting with the N-terminus of eIF3j. Further, eIF3j occupied the mRNA entry channel via its ultimate C-terminus providing a structural explanation for its antagonistic role with respect to mRNA binding. Overall, the native human samples provide a near-complete molecular picture of the architecture and sophisticated interaction network of the 43S-bound eIF3 complex and the eIF2 ternary complex containing the initiator tRNA.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Assembly

Deposited unit
a: 40S ribosomal protein SA
p: 40S ribosomal protein S3a
d: 40S ribosomal protein S2
Q: 40S ribosomal protein S26
q: 40S ribosomal protein S4, X isoform
W: 60S ribosomal protein L41
r: 40S ribosomal protein S6
s: 40S ribosomal protein S7
t: 40S ribosomal protein S8
c: 40S ribosomal protein S9
n: 40S ribosomal protein S11
m: 40S ribosomal protein S13
i: 40S ribosomal protein S14
y: 40S ribosomal protein S21
f: 40S ribosomal protein S15a
j: 40S ribosomal protein S23
z: 40S ribosomal protein S24
R: 40S ribosomal protein S27
T: 40S ribosomal protein S30
2: 18S ribosomal RNA
w: 40S ribosomal protein S17
g: 40S ribosomal protein S16
b: 40S ribosomal protein S3
e: 40S ribosomal protein S5
u: 40S ribosomal protein S10
v: 40S ribosomal protein S12
o: 40S ribosomal protein S15
k: 40S ribosomal protein S18
x: 40S ribosomal protein S19
h: 40S ribosomal protein S20
P: 40S ribosomal protein S25
S: 40S ribosomal protein S28
l: 40S ribosomal protein S29
U: Ubiquitin-40S ribosomal protein S27a
V: Receptor of activated protein C kinase 1
I: Eukaryotic translation initiation factor 3 subunit I
B: Eukaryotic translation initiation factor 3 subunit B
A: Eukaryotic translation initiation factor 3 subunit A
C: Eukaryotic translation initiation factor 3 subunit C
E: Eukaryotic translation initiation factor 3 subunit E
F: Eukaryotic translation initiation factor 3 subunit F
H: Eukaryotic translation initiation factor 3 subunit H
K: Eukaryotic translation initiation factor 3 subunit K
L: Eukaryotic translation initiation factor 3 subunit L
M: Eukaryotic translation initiation factor 3 subunit M
1: ATP-binding cassette sub-family E member 1
N: Eukaryotic translation initiation factor 1
D: Eukaryotic translation initiation factor 3 subunit D
Y: RNA recognition motif (unknown)
G: Eukaryotic translation initiation factor 3 subunit J
J: Eukaryotic translation initiation factor 3 subunit J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,804,81860
Polymers1,802,93651
Non-polymers1,8829
Water0
1


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

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Components

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40S ribosomal protein ... , 31 types, 31 molecules apdQqrstcnmiyfjzRTwgbeuvokxhPSl

#1: 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: 24260.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#2: Protein 40S ribosomal protein S3a / / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 24560.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#3: Protein 40S ribosomal protein S2 / / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 23861.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#4: Protein 40S ribosomal protein S26 / / Small ribosomal subunit protein eS26


Mass: 11645.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#5: Protein 40S ribosomal protein S4, X isoform / Ribosome / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 28892.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#7: Protein 40S ribosomal protein S6 / / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 25612.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#8: Protein 40S ribosomal protein S7 / / Small ribosomal subunit protein eS7


Mass: 20788.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#9: Protein 40S ribosomal protein S8 / / Small ribosomal subunit protein eS8


Mass: 23945.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#10: Protein 40S ribosomal protein S9 / / Small ribosomal subunit protein uS4


Mass: 21279.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#11: Protein 40S ribosomal protein S11 / / Small ribosomal subunit protein uS17


Mass: 16913.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#12: 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
#13: Protein 40S ribosomal protein S14 /


Mass: 13463.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A0A2R8Y811
#14: Protein 40S ribosomal protein S21 / / Small ribosomal subunit protein eS21


Mass: 8977.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#15: 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
#16: 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
#17: Protein 40S ribosomal protein S24 /


Mass: 14259.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: E7ETK0
#18: Protein 40S ribosomal protein S27 / / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9210.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#19: Protein/peptide 40S ribosomal protein S30 / / Small ribosomal subunit protein eS30


Mass: 5069.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#21: Protein 40S ribosomal protein S17 / / Small ribosomal subunit protein eS17


Mass: 15036.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#22: Protein 40S ribosomal protein S16 / / Small ribosomal subunit protein uS9


Mass: 15637.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#23: Protein 40S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 24871.156 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
#24: Protein 40S ribosomal protein S5 / / Small ribosomal subunit protein uS7


Mass: 21327.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#25: Protein 40S ribosomal protein S10 / / Small ribosomal subunit protein eS10


Mass: 11372.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#26: Protein 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 12945.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#27: Protein 40S ribosomal protein S15 / / RIG protein / Small ribosomal subunit protein uS19


Mass: 14010.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#28: Protein 40S ribosomal protein S18 / / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 16496.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#29: Protein 40S ribosomal protein S19 / / Small ribosomal subunit protein eS19


Mass: 15563.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#30: Protein 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 11186.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#31: Protein 40S ribosomal protein S25 / / Small ribosomal subunit protein eS25


Mass: 7938.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#32: Protein 40S ribosomal protein S28 / / Small ribosomal subunit protein eS28


Mass: 6878.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#33: Protein 40S ribosomal protein S29 / / Small ribosomal subunit protein uS14


Mass: 6444.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273

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Protein , 5 types, 5 molecules UV1NY

#34: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 7257.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979
#35: 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: 34224.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#46: Protein ATP-binding cassette sub-family E member 1 / 2'-5'-oligoadenylate-binding protein / HuHP68 / RNase L inhibitor / Ribonuclease 4 inhibitor / RNS4I


Mass: 66972.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61221
#47: Protein Eukaryotic translation initiation factor 1 / eIF1 / A121 / Protein translation factor SUI1 homolog / Sui1iso1


Mass: 10388.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41567
#49: Protein RNA recognition motif (unknown)


Mass: 5562.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Eukaryotic translation initiation factor 3 subunit ... , 12 types, 13 molecules IBACEFHKLMDGJ

#36: Protein Eukaryotic translation initiation factor 3 subunit I / eIF3i / Eukaryotic translation initiation factor 3 subunit 2 / TGF-beta receptor-interacting ...eIF3i / Eukaryotic translation initiation factor 3 subunit 2 / TGF-beta receptor-interacting protein 1 / TRIP-1 / eIF-3-beta / eIF3 p36


Mass: 35352.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13347
#37: Protein Eukaryotic translation initiation factor 3 subunit B / eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / Prt1 homolog / hPrt1 / eIF-3-eta / ...eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / Prt1 homolog / hPrt1 / eIF-3-eta / eIF3 p110 / eIF3 p116


Mass: 65901.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55884
#38: Protein Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 ...eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 / eIF3 p185


Mass: 85564.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14152
#39: Protein Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


Mass: 86197.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: B4DVU3
#40: Protein Eukaryotic translation initiation factor 3 subunit E / eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 ...eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 homolog / eIF-3 p48


Mass: 50438.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60228
#41: Protein Eukaryotic translation initiation factor 3 subunit F / eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF- ...eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF-3-epsilon / eIF3 p47


Mass: 29836.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00303, ubiquitinyl hydrolase 1
#42: Protein Eukaryotic translation initiation factor 3 subunit H / eIF3h / Eukaryotic translation initiation factor 3 subunit 3 / eIF-3-gamma / eIF3 p40 subunit


Mass: 36960.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15372
#43: Protein Eukaryotic translation initiation factor 3 subunit K / eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / ...eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / PLAC-24 / eIF-3 p25 / eIF-3 p28


Mass: 24952.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UBQ5
#44: Protein Eukaryotic translation initiation factor 3 subunit L / eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic ...eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic translation initiation factor 3 subunit E-interacting protein


Mass: 44172.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y262
#45: Protein Eukaryotic translation initiation factor 3 subunit M / eIF3m / Fetal lung protein B5 / hFL-B5 / PCI domain-containing protein 1


Mass: 41278.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7L2H7
#48: Protein Eukaryotic translation initiation factor 3 subunit D / eIF3d / Eukaryotic translation initiation factor 3 subunit 7 / eIF-3-zeta / eIF3 p66


Mass: 61489.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15371
#50: Protein Eukaryotic translation initiation factor 3 subunit J / eIF3j / Eukaryotic translation initiation factor 3 subunit 1 / eIF-3-alpha / eIF3 p35


Mass: 29108.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75822

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Protein/peptide / RNA chain , 2 types, 2 molecules W2

#20: RNA chain 18S ribosomal RNA /


Mass: 555210.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#6: Protein/peptide 60S ribosomal protein L41 / / HG12 / Large ribosomal subunit protein eL41


Mass: 3344.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945

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Non-polymers , 5 types, 9 molecules

#51: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#52: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#53: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#54: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#55: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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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: ABCE1-bound 43S initiation complex / Type: RIBOSOME / Entity ID: #1-#50 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 48 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5231 / Symmetry type: POINT
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 19.98 Å2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0099120672
ELECTRON MICROSCOPYf_angle_d1.3374171402
ELECTRON MICROSCOPYf_chiral_restr0.068220736
ELECTRON MICROSCOPYf_plane_restr0.008815553
ELECTRON MICROSCOPYf_dihedral_angle_d19.973650316

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