3V11

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.262 

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

  • 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 fo ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 2 subunit gamma
A
414Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: eif2g
Find proteins for Q980A5 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q980A5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 2 subunit alpha
B
266Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: eif2a (aif2a)
Find proteins for Q97Z79 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97Z79
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor 2 subunit beta
C
138Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: eif2b (aif2b)
Find proteins for Q97W59 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97W59
Entity ID: 4
MoleculeChainsLengthOrganism
Initiator tRNAD77Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
MET
Query on MET

Download SDF File 
Download CCD File 
D
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
D
RNA LINKINGC9 H13 N2 O9 PU
OMC
Query on OMC
D
RNA LINKINGC10 H16 N3 O8 PC
4SU
Query on 4SU
D
RNA LINKINGC9 H13 N2 O8 P SU
5MU
Query on 5MU
D
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
D
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.262 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 133.000α = 90.00
b = 133.000β = 90.00
c = 167.200γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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