4KZX

Rabbit 40S ribosomal subunit in complex with eIF1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.81 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.347 
  • R-Value Observed: 0.347 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The initiation of mammalian protein synthesis and mRNA scanning mechanism.

Lomakin, I.B.Steitz, T.A.

(2013) Nature 500: 307-311

  • DOI: https://doi.org/10.1038/nature12355
  • Primary Citation of Related Structures:  
    4KZX, 4KZY, 4KZZ

  • PubMed Abstract: 

    During translation initiation in eukaryotes, the small ribosomal subunit binds messenger RNA at the 5' end and scans in the 5' to 3' direction to locate the initiation codon, form the 80S initiation complex and start protein synthesis. This simple, yet intricate, process is guided by multiple initiation factors. Here we determine the structures of three complexes of the small ribosomal subunit that represent distinct steps in mammalian translation initiation. These structures reveal the locations of eIF1, eIF1A, mRNA and initiator transfer RNA bound to the small ribosomal subunit and provide insights into the details of translation initiation specific to eukaryotes. Conformational changes associated with the captured functional states reveal the dynamics of the interactions in the P site of the ribosome. These results have functional implications for the mechanism of mRNA scanning.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA. ivan.lomakin@yale.edu


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SA295Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3a264Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TN72 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2278Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U2Z9 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3243Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4X263Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6249Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S9194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10165Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T168 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12132Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14151Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T1F0 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16146Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SGX4 (Oryctolagus cuniculus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17135Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18152Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19145Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20119Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SIZ2 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2183Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TM82 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15A130Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23143Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24133Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TS40 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26AA [auth a]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27BA [auth b]84Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28CA [auth c]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29DA [auth d]56Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30EA [auth e]133Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27AFA [auth f]156Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein RACK1GA [auth g]317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1IA [auth l]113Homo sapiensMutation(s): 0 
Gene Names: EIF1SUI1
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PHAROS:  P41567
GTEx:  ENSG00000173812 
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Entity ID: 34
MoleculeChains LengthOrganismImage
18S ribosomal RNAHA [auth i]1,863Oryctolagus cuniculus
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.81 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.347 
  • R-Value Observed: 0.347 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 292.121α = 90
b = 292.121β = 90
c = 477.667γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-08-07
    Changes: Database references
  • Version 1.2: 2013-09-04
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description