3V11

Structure of the ternary initiation complex AIF2:GDPNP:methionylated initiator TRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the ternary initiation complex aIF2-GDPNP-methionylated initiator tRNA.

Schmitt, E.Panvert, M.Lazennec-Schurdevin, C.Coureux, P.D.Perez, J.Thompson, A.Mechulam, Y.

(2012) Nat Struct Mol Biol 19: 450-454

  • DOI: 10.1038/nsmb.2259
  • Primary Citation of Related Structures:  
    3V11

  • PubMed Abstract: 
  • Eukaryotic and archaeal translation initiation factor 2 (e/aIF2) is a heterotrimeric GTPase that has a crucial role in the selection of the correct start codon on messenger RNA. We report the 5-Å resolution crystal structure of the ternary complex formed by archaeal aIF2 from Sulfolobus solfataricus, the GTP analog GDPNP and methionylated initiator tRNA ...

    Eukaryotic and archaeal translation initiation factor 2 (e/aIF2) is a heterotrimeric GTPase that has a crucial role in the selection of the correct start codon on messenger RNA. We report the 5-Å resolution crystal structure of the ternary complex formed by archaeal aIF2 from Sulfolobus solfataricus, the GTP analog GDPNP and methionylated initiator tRNA. The 3D model is further supported by solution studies using small-angle X-ray scattering. The tRNA is bound by the α and γ subunits of aIF2. Contacts involve the elbow of the tRNA and the minor groove of the acceptor stem, but not the T-stem minor groove. We conclude that despite considerable structural homology between the core γ subunit of aIF2 and the elongation factor EF1A, these two G proteins of the translation apparatus use very different tRNA-binding strategies.


    Organizational Affiliation

    Laboratoire de Biochimie, Unité mixte de Recherche 7654, Ecole Polytechnique, Centre National de la Recherche Scientifique, Palaiseau, France. emma@botrytis.polytechnique.fr



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor 2 subunit gammaA414Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: eif2gSSO0412
EC: 3.6.5.3
UniProt
Find proteins for Q980A5 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q980A5 
Go to UniProtKB:  Q980A5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ980A5
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor 2 subunit alphaB266Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: eif2aSSO1050aif2a
UniProt
Find proteins for Q97Z79 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97Z79 
Go to UniProtKB:  Q97Z79
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UniProt GroupQ97Z79
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Translation initiation factor 2 subunit betaC138Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: eif2bSSO2381aif2b
UniProt
Find proteins for Q97W59 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97W59 
Go to UniProtKB:  Q97W59
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UniProt GroupQ97W59
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
Initiator tRNAD77Escherichia coli
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
F [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
MET
Query on MET

Download Ideal Coordinates CCD File 
G [auth D]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
MG
Query on MG

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E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.265 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133α = 90
b = 133β = 90
c = 167.2γ = 120
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-28
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description