7A1G

Structure of a crosslinked yeast ABCE1-bound 43S pre-initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A structural inventory of native ribosomal ABCE1-43S pre-initiation complexes.

Kratzat, H.Mackens-Kiani, T.Ameismeier, M.Potocnjak, M.Cheng, J.Dacheux, E.Namane, A.Berninghausen, O.Herzog, F.Fromont-Racine, M.Becker, T.Beckmann, R.

(2021) EMBO J 40: e105179-e105179

  • DOI: https://doi.org/10.15252/embj.2020105179
  • Primary Citation of Related Structures:  
    6ZCE, 6ZU9, 6ZVJ, 7A09, 7A1G

  • PubMed 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. 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.


  • Organizational Affiliation

    Génétique des Interactions Macromoléculaires, UMR3525 CNRS, Institut Pasteur, Paris, France.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0-AB [auth P]206Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1-AC [auth Q]232Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2D [auth R]216Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4-AE [auth S]258Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6-AF [auth T]228Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7-AG [auth U]184Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8-AH [auth V]200Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9-AI [auth W]184Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11-AJ [auth X]142Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13K [auth Y]150Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14-BL [auth Z]127Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21-AM [auth a]87Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22-AN [auth b]129Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23-AO [auth c]144Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24-AP [auth d]134Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26-BQ [auth e]97Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27-AR [auth f]81Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30-AS [auth g]60Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15T [auth E]117Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3U [auth A]222Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5V [auth B]206Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10-AW [auth C]92Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12X [auth D]121Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16-AY [auth F]141Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17-BZ [auth H]125Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18-AAA [auth I]145Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19-ABA [auth J]143Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20CA [auth K]100Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25-ADA [auth L]82Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29-AEA [auth M]53Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31FA [auth N]73Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinGA [auth O]312Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28-AHA [auth h]63Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit JIA [auth z],
JA [auth y]
265Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor RLI1KA [auth x]601Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S ribosomal RNAA [auth 2]1,771Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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QD [auth x]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4
Query on SF4

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OD [auth x],
PD [auth x]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
MD [auth M],
ND [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth 2]
AC [auth 2]
AD [auth 2]
BB [auth 2]
BC [auth 2]
AB [auth 2],
AC [auth 2],
AD [auth 2],
BB [auth 2],
BC [auth 2],
BD [auth 2],
CB [auth 2],
CC [auth 2],
CD [auth 2],
DB [auth 2],
DC [auth 2],
DD [auth 2],
EB [auth 2],
EC [auth 2],
ED [auth 2],
FB [auth 2],
FC [auth 2],
FD [auth 2],
GB [auth 2],
GC [auth 2],
GD [auth 2],
HB [auth 2],
HC [auth 2],
HD [auth 2],
IB [auth 2],
IC [auth 2],
ID [auth 2],
JB [auth 2],
JC [auth 2],
JD [auth R],
KB [auth 2],
KC [auth 2],
KD [auth S],
LA [auth 2],
LB [auth 2],
LC [auth 2],
LD [auth B],
MA [auth 2],
MB [auth 2],
MC [auth 2],
NA [auth 2],
NB [auth 2],
NC [auth 2],
OA [auth 2],
OB [auth 2],
OC [auth 2],
PA [auth 2],
PB [auth 2],
PC [auth 2],
QA [auth 2],
QB [auth 2],
QC [auth 2],
RA [auth 2],
RB [auth 2],
RC [auth 2],
RD [auth x],
SA [auth 2],
SB [auth 2],
SC [auth 2],
TA [auth 2],
TB [auth 2],
TC [auth 2],
UA [auth 2],
UB [auth 2],
UC [auth 2],
VA [auth 2],
VB [auth 2],
VC [auth 2],
WA [auth 2],
WB [auth 2],
WC [auth 2],
XA [auth 2],
XB [auth 2],
XC [auth 2],
YA [auth 2],
YB [auth 2],
YC [auth 2],
ZA [auth 2],
ZB [auth 2],
ZC [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references
  • Version 1.2: 2021-01-13
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references