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- PDB-7a1g: Structure of a crosslinked yeast ABCE1-bound 43S pre-initiation c... -

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Entry
Database: PDB / ID: 7a1g
TitleStructure of a crosslinked yeast ABCE1-bound 43S pre-initiation complex
Components
  • (40S ribosomal protein ...) x 31
  • 18S ribosomal RNA
  • Eukaryotic translation initiation factor 3 subunit J
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Translation initiation factor RLI1
  • Ubiquitin-40S ribosomal protein S31
KeywordsRIBOSOME / Translation / Initiation / Ribosome Recycling / ABC Proteins
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex / ribosome disassembly / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / regulation of cellular response to stress / invasive growth in response to glucose limitation ...eukaryotic translation initiation factor 3 complex / ribosome disassembly / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / regulation of cellular response to stress / invasive growth in response to glucose limitation / GDP-dissociation inhibitor activity / rRNA export from nucleus / ribosomal subunit export from nucleus / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / mRNA destabilization / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / rRNA methylation / rescue of stalled ribosome / G-protein alpha-subunit 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 / ribosomal small subunit export from nucleus / ribosomal small subunit binding / maturation of SSU-rRNA / regulation of translational fidelity / ribosomal large subunit biogenesis / small-subunit processome / ribosomal small subunit biogenesis / protein kinase A catalytic subunit binding / positive regulation of protein kinase activity / cellular response to amino acid starvation / translation initiation factor activity / translational initiation / ribosome assembly / maintenance of translational fidelity / positive regulation of translational fidelity / translational termination / protein kinase C binding / positive regulation of translation / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / modification-dependent protein catabolic process / small ribosomal subunit rRNA binding / mRNA 5'-UTR binding / protein tag / rRNA processing / cytoplasmic stress granule / cytoplasmic translation / ribosome binding / ribosome biogenesis / cytosolic small ribosomal subunit / small ribosomal subunit / protein localization / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / protein ubiquitination / translation / negative regulation of gene expression / iron ion binding / ATPase / positive regulation of protein phosphorylation / mRNA binding / G protein-coupled receptor signaling pathway / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Translation initiation factor eIF3 subunit / Ubiquitin conserved site / Ribosomal protein S4e, N-terminal, 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 ...Translation initiation factor eIF3 subunit / Ubiquitin conserved site / Ribosomal protein S4e, N-terminal, 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 S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / WD40 repeat, conserved site / Ubiquitin domain / Ribosomal protein S2, conserved site / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal protein S15P / Eukaryotic translation initiation factor 3-like domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal S11, conserved site / P-loop containing nucleoside triphosphate hydrolase / RLI1 / Ribosomal protein S10, eukaryotic/archaeal / KOW / Ribosomal protein S12/S23 / Ribosomal protein S30 / RNase L inhibitor RLI-like, possible metal-binding domain / K homology domain superfamily, prokaryotic type / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S5, N-terminal / Ribosomal S24e conserved site / Ribosomal protein S4e, N-terminal / Eukaryotic translation initiation factor 3 subunit J / Ribosomal protein S6, eukaryotic / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L2, domain 2 / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / ABC transporter, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal protein S7 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S19A/S15e / Ribosomal protein S8e / Ribosomal protein S9/S16 / Ribosomal protein S13/S18 / Ribosomal protein S10p/S20e / Ribosomal protein S27a / WD domain, G-beta repeat / Ribosomal S3Ae family / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / KOW motif / Ribosomal family S4e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S7e / S4 domain / KH domain / Ribosomal protein S17 / Ribosomal_S17 N-terminal / Ribosomal protein S15 / Ribosomal protein S11 / Ribosomal protein S21e / Ribosomal protein S8 / Ribosomal protein S12/S23 / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S30 / Ribosomal protein S28e / 4Fe-4S binding domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S3, C-terminal domain / Ribosomal protein S10 domain / Winged helix DNA-binding domain superfamily / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S11, N-terminal
40S ribosomal protein S30-A / 40S ribosomal protein S6-A / 40S ribosomal protein S4-A / 40S ribosomal protein S13 / 40S ribosomal protein S24-A / Ubiquitin-40S ribosomal protein S31 / 40S ribosomal protein S22-A / 40S ribosomal protein S9-A / 40S ribosomal protein S21-A / 40S ribosomal protein S19-A ...40S ribosomal protein S30-A / 40S ribosomal protein S6-A / 40S ribosomal protein S4-A / 40S ribosomal protein S13 / 40S ribosomal protein S24-A / Ubiquitin-40S ribosomal protein S31 / 40S ribosomal protein S22-A / 40S ribosomal protein S9-A / 40S ribosomal protein S21-A / 40S ribosomal protein S19-A / 40S ribosomal protein S3 / 40S ribosomal protein S23-A / 40S ribosomal protein S17-B / 40S ribosomal protein S2 / 40S ribosomal protein S26-B / 40S ribosomal protein S5 / 40S ribosomal protein S7-A / 40S ribosomal protein S0-A / 40S ribosomal protein S1-A / 40S ribosomal protein S27-A / Guanine nucleotide-binding protein subunit beta-like protein / 40S ribosomal protein S20 / 40S ribosomal protein S14-B / 40S ribosomal protein S29-A / 40S ribosomal protein S8-A / 40S ribosomal protein S12 / Translation initiation factor RLI1 / Eukaryotic translation initiation factor 3 subunit J / 40S ribosomal protein S10-A / 40S ribosomal protein S25-A / 40S ribosomal protein S28-A / 40S ribosomal protein S18-A / 40S ribosomal protein S16-A / 40S ribosomal protein S11-A / 40S ribosomal protein S15
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsMackens-Kiani, T. / Kratzat, H. / 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
DepositionAug 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 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
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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Assembly

Deposited unit
2: 18S ribosomal RNA
P: 40S ribosomal protein S0-A
Q: 40S ribosomal protein S1-A
R: 40S ribosomal protein S2
S: 40S ribosomal protein S4-A
T: 40S ribosomal protein S6-A
U: 40S ribosomal protein S7-A
V: 40S ribosomal protein S8-A
W: 40S ribosomal protein S9-A
X: 40S ribosomal protein S11-A
Y: 40S ribosomal protein S13
Z: 40S ribosomal protein S14-B
a: 40S ribosomal protein S21-A
b: 40S ribosomal protein S22-A
c: 40S ribosomal protein S23-A
d: 40S ribosomal protein S24-A
e: 40S ribosomal protein S26-B
f: 40S ribosomal protein S27-A
g: 40S ribosomal protein S30-A
E: 40S ribosomal protein S15
A: 40S ribosomal protein S3
B: 40S ribosomal protein S5
C: 40S ribosomal protein S10-A
D: 40S ribosomal protein S12
F: 40S ribosomal protein S16-A
H: 40S ribosomal protein S17-B
I: 40S ribosomal protein S18-A
J: 40S ribosomal protein S19-A
K: 40S ribosomal protein S20
L: 40S ribosomal protein S25-A
M: 40S ribosomal protein S29-A
N: Ubiquitin-40S ribosomal protein S31
O: Guanine nucleotide-binding protein subunit beta-like protein
h: 40S ribosomal protein S28-A
z: Eukaryotic translation initiation factor 3 subunit J
y: Eukaryotic translation initiation factor 3 subunit J
x: Translation initiation factor RLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,246,021122
Polymers1,242,81637
Non-polymers3,20685
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 1 types, 1 molecules 2

#1: RNA chain 18S ribosomal RNA /


Mass: 570585.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast)

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

#2: Protein 40S ribosomal protein S0-A / Ribosome / Nucleic acid-binding protein NAB1A / Small ribosomal subunit protein uS2-A


Mass: 22811.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32905
#3: Protein 40S ribosomal protein S1-A / Ribosome / RP10A / Small ribosomal subunit protein eS1-A


Mass: 26314.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33442
#4: Protein 40S ribosomal protein S2 / / Omnipotent suppressor protein SUP44 / RP12 / S4 / Small ribosomal subunit protein uS5 / YS5


Mass: 23084.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25443
#5: Protein 40S ribosomal protein S4-A / Ribosome / RP5 / S7 / Small ribosomal subunit protein eS4-A / YS6


Mass: 29167.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX35
#6: Protein 40S ribosomal protein S6-A / Ribosome / RP9 / S10 / Small ribosomal subunit protein eS6-A / YS4


Mass: 26181.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX37
#7: Protein 40S ribosomal protein S7-A / Ribosome / RP30 / RP40 / Small ribosomal subunit protein eS7-A


Mass: 21000.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26786
#8: Protein 40S ribosomal protein S8-A / Ribosome / RP19 / S14 / Small ribosomal subunit protein eS8-A / YS9


Mass: 22537.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX39
#9: Protein 40S ribosomal protein S9-A / Ribosome / RP21 / S13 / Small ribosomal subunit protein uS4-A / YP28 / YS11


Mass: 21081.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: O13516
#10: Protein 40S ribosomal protein S11-A / Ribosome / RP41 / S18 / Small ribosomal subunit protein uS17-A / YS12


Mass: 16272.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX47
#11: Protein 40S ribosomal protein S13 / / S27a / Small ribosomal subunit protein uS15 / YS15


Mass: 16928.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05756
#12: Protein 40S ribosomal protein S14-B / Ribosome / RP59B / Small ribosomal subunit protein uS11-B


Mass: 13446.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39516
#13: Protein 40S ribosomal protein S21-A / Ribosome / S26 / Small ribosomal subunit protein eS21-A / YS25


Mass: 9758.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0V8
#14: Protein 40S ribosomal protein S22-A / Ribosome / RP50 / S24 / Small ribosomal subunit protein uS8-A / YP58 / YS22


Mass: 14518.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C0W1
#15: Protein 40S ribosomal protein S23-A / Ribosome / RP37 / S28 / Small ribosomal subunit protein uS12-A / YS14


Mass: 15942.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX29
#16: Protein 40S ribosomal protein S24-A / Ribosome / RP50 / Small ribosomal subunit protein eS24-A


Mass: 15231.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX31
#17: Protein 40S ribosomal protein S26-B / Ribosome / Small ribosomal subunit protein eS26-B


Mass: 11022.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P39939
#18: Protein 40S ribosomal protein S27-A / Ribosome / RP61 / Small ribosomal subunit protein eS27-A / YS20


Mass: 8762.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P35997
#19: Protein 40S ribosomal protein S30-A / Ribosome / Small ribosomal subunit protein eS30-A


Mass: 6779.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX33
#20: Protein 40S ribosomal protein S15 / / RIG protein / RP52 / S21 / Small ribosomal subunit protein uS19 / YS21


Mass: 13265.591 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q01855
#21: Protein 40S ribosomal protein S3 / / RP13 / Small ribosomal subunit protein uS3 / YS3


Mass: 24631.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05750
#22: Protein 40S ribosomal protein S5 / / RP14 / S2 / Small ribosomal subunit protein uS7 / YS8


Mass: 22908.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P26783
#23: Protein 40S ribosomal protein S10-A / Ribosome / Small ribosomal subunit protein eS10-A


Mass: 11042.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q08745
#24: Protein 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 13028.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P48589
#25: Protein 40S ribosomal protein S16-A / Ribosome / RP61R / Small ribosomal subunit protein uS9-A


Mass: 15659.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX51
#26: Protein 40S ribosomal protein S17-B / Ribosome / RP51B / Small ribosomal subunit protein eS17-B


Mass: 14268.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P14127
#27: Protein 40S ribosomal protein S18-A / Ribosome / Small ribosomal subunit protein uS13-A


Mass: 16940.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0CX55
#28: Protein 40S ribosomal protein S19-A / Ribosome / RP55A / S16a / Small ribosomal subunit protein eS19-A / YP45 / YS16A


Mass: 15810.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P07280
#29: Protein 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 11363.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38701
#30: Protein 40S ribosomal protein S25-A / Ribosome / RP45 / S31 / Small ribosomal subunit protein eS25-A / YS23


Mass: 9540.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E792
#31: Protein 40S ribosomal protein S29-A / Ribosome / S36 / Small ribosomal subunit protein uS14-A / YS29


Mass: 6335.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P41057
#34: Protein 40S ribosomal protein S28-A / Ribosome / S33 / Small ribosomal subunit protein eS28-A / YS27


Mass: 7116.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E7X9

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Protein , 4 types, 5 molecules NOzyx

#32: Protein Ubiquitin-40S ribosomal protein S31


Mass: 8388.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P05759
#33: Protein Guanine nucleotide-binding protein subunit beta-like protein / Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ...Receptor for activated C kinase / Receptor of activated protein kinase C 1 / RACK1 / Small ribosomal subunit protein RACK1


Mass: 34151.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38011
#35: Protein Eukaryotic translation initiation factor 3 subunit J / eIF3j / Eukaryotic translation initiation factor 3 30 kDa subunit / eIF-3 30 kDa


Mass: 29611.225 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q05775
#36: Protein Translation initiation factor RLI1 / ATP-binding cassette sub-family E member RLI1 / RNase L inhibitor


Mass: 67714.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03195

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Non-polymers , 4 types, 85 molecules

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


Mass: 24.305 Da / Num. of mol.: 80 / Source method: obtained synthetically / Formula: Mg
#38: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#39: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#40: 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

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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 PIC / Type: RIBOSOME / Entity ID: #1-#36 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Buffer solutionpH: 7.4
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: 44.8 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 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25245 / Symmetry type: POINT
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 13.27 Å2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009187007
ELECTRON MICROSCOPYf_angle_d1.2527126130
ELECTRON MICROSCOPYf_chiral_restr0.068615698
ELECTRON MICROSCOPYf_plane_restr0.00919479
ELECTRON MICROSCOPYf_dihedral_angle_d20.487438376

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