5K0Y

m48S late-stage initiation complex, purified from rabbit reticulocytes lysates, displaying eIF2 ternary complex and eIF3 i and g subunits relocated to the intersubunit face


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 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

eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition.

Simonetti, A.Brito Querido, J.Myasnikov, A.G.Mancera-Martinez, E.Renaud, A.Kuhn, L.Hashem, Y.

(2016) Mol Cell 63: 206-217

  • DOI: https://doi.org/10.1016/j.molcel.2016.05.033
  • Primary Citation of Related Structures:  
    5K0Y, 5K1H

  • PubMed Abstract: 

    mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal 40S subunit, mRNA scanning for start codon, and accommodation of initiator tRNA at the 40S P site. eIF3, composed of 13 subunits, 8 core (a, c, e, f, h, l, k, and m) and 5 peripheral (b, d, g, i, and j), plays a central role during this process. Here we report a cryo-electron microscopy structure of a mammalian 48S initiation complex at 5.8 Å resolution. It shows the relocation of subunits eIF3i and eIF3g to the 40S intersubunit face on the GTPase binding site, at a late stage in initiation. On the basis of a previous study, we demonstrate the relocation of eIF3b to the 40S intersubunit face, binding below the eIF2-Met-tRNAi(Met) ternary complex upon mRNA attachment. Our analysis reveals the deep rearrangement of eIF3 and unravels the molecular mechanism underlying eIF3 function in mRNA scanning and timing of ribosomal subunit joining.


  • Organizational Affiliation

    CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France. Electronic address: a.simonetti@ibmc-cnrs.unistra.fr.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1D [auth P]266Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF2S1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS17E [auth G]158Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100347468
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Find proteins for G1TRM4 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS9F [auth H]141Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS16
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4G [auth I]263Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS4X
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS14H [auth J]53Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9 (Predicted)I [auth K]182Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS13J [auth L]137Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS18
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit GK [auth M]38Homo sapiensMutation(s): 0 
Gene Names: EIF3GEIF3S4
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GTEx:  ENSG00000130811 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit GL [auth O]77Homo sapiensMutation(s): 0 
Gene Names: EIF3GEIF3S4
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GTEx:  ENSG00000130811 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS12M [auth Q]142Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS19N [auth R]141Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345774
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Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
eukaryotic initiation factor 2 Gamma subunit (eIF2-Gamma)O [auth S]422Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit IP [auth T]329Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3IEIF3S2
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS7Q [auth U]191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS30R [auth V]59Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS25S [auth W]75Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS25
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS7T [auth X]190Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS7
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27U [auth Y]84Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS27
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Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS15V [auth Z]150Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS13
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS8W [auth a]129Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
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Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21X [auth b]82Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS21
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS5Y [auth c]226Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
eukaryotic initiation factor 2 subunit Beta (eIF2-Beta)Z [auth d]17Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for Q97W59 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS17AA [auth e]126Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS17
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS2BA [auth f]208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS3CA [auth g]227Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS10DA [auth h]104Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS1EA [auth i]215Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS11FA [auth j]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS26GA [auth k]99Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS26
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS28HA [auth l]64Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein RACK1IA [auth m]313Oryctolagus cuniculusMutation(s): 0 
Gene Names: GNB2L1
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS19JA [auth n]127Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC103349305
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8KA [auth o]206Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS8
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS31LA [auth p]71Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348379
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6MA [auth q]237Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100339133RPS6
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12NA [auth r]124Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24OA [auth s]131Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS24
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS10PA [auth t]98Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS10
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Find proteins for G1T168 (Oryctolagus cuniculus)
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Entity ID: 1
MoleculeChains LengthOrganismImage
tRNAA [auth N]75Oryctolagus cuniculus
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S ribosomal RNAB [auth A]1,776Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
mRNAC [auth F]30Oryctolagus cuniculus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.3
MODEL REFINEMENTVMD

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceatRAction program ANR CryoEM80S
French National Research AgencyFranceANR-10-LABX-0036_NETRNA

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-08-03
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.3: 2018-04-18
    Changes: Data collection, Structure summary