4KZZ

Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and eIF1A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.03 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.345 
  • R-Value Observed: 0.345 

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, yet i ...

    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 SA A295Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSA
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S3A B264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S2 C278Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S3 D243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S4X E263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S5 F204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S6 G249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S7 H194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
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40S Ribosomal Protein S8 I208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S9 J194Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S10 K165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S11 L158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S12 M132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S13 N151Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS13
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S14 O151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S15 P145Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S16 Q146Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S17 R135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S18 S152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
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40S Ribosomal Protein S19 T145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S20 U119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S21 V83Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS21
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S15A W130Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
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40S Ribosomal Protein S23 X143Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S24 Y133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S25 Z125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S26 a115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S27 b84Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S28 c69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S29 d56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S30 e133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein S27A f156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S Ribosomal Protein RACK1 g317Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
human initiation factor eIF1A n144Homo sapiensMutation(s): 0 
Gene Names: EIF1AX, EIF1A, EIF4C
Find proteins for P47813 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS:  P47813
GTEx:  ENSG00000173674
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Entity ID: 34
MoleculeChainsLengthOrganismImage
18S Ribosomal RNAi1863Oryctolagus cuniculus
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Entity ID: 35
MoleculeChainsLengthOrganismImage
initiator Met-RNA-ij75Homo sapiens
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Entity ID: 36
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mRNAk24synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.03 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.345 
  • R-Value Observed: 0.345 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 297.75α = 90
b = 297.75β = 90
c = 485.16γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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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