4KZY

Rabbit 40S ribosomal subunit in complex with eIF1 and eIF1A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.01 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.366 
  • R-Value Observed: 0.365 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 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, y ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein SAA295Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSA
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S3AB264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S2C278Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S3D243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S4XE263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S5F204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S6G249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S7H194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S8I208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S9J194Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S10K165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S11L158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S12M132Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S13N151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S14O151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S15P145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S16Q146Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S17R135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S18S152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S19T145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S20U119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S21V83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S15AW130Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S23X143Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S24Y133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S25Z125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S26a115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S27b84Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S28c69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S29d56Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S30e133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S27Af156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein RACK1g317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
human initiation factor eIF1l113Homo sapiensMutation(s): 0 
Gene Names: EIF1SUI1
Find proteins for P41567 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  P41567
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
human initiation factor eIF1An144Homo sapiensMutation(s): 0 
Gene Names: EIF1AXEIF1AEIF4C
Find proteins for P47813 (Homo sapiens)
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PHAROS  P47813
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Entity ID: 34
MoleculeChainsLengthOrganismImage
18S Ribosomal RNAi1863Oryctolagus cuniculus
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.01 Å
  • R-Value Free: 0.348 
  • R-Value Work: 0.366 
  • R-Value Observed: 0.365 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 296.897α = 90
b = 296.897β = 90
c = 478.305γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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