Crystal Structure of Thermus Thermophilus IF2, Apo and GDP-bound Forms (2-474)

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 

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Initiation factor 2 crystal structure reveals a different domain organization from eukaryotic initiation factor 5B and mechanism among translational GTPases.

Eiler, D.Lin, J.Simonetti, A.Klaholz, B.P.Steitz, T.A.

(2013) Proc Natl Acad Sci U S A 110: 15662-15667

  • DOI: https://doi.org/10.1073/pnas.1309360110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The initiation of protein synthesis uses initiation factor 2 (IF2) in prokaryotes and a related protein named eukaryotic initiation factor 5B (eIF5B) in eukaryotes. IF2 is a GTPase that positions the initiator tRNA on the 30S ribosomal initiation complex and stimulates its assembly to the 50S ribosomal subunit to make the 70S ribosome. The 3.1-Å resolution X-ray crystal structures of the full-length Thermus thermophilus apo IF2 and its complex with GDP presented here exhibit two different conformations (all of its domains except C2 domain are visible). Unlike all other translational GTPases, IF2 does not have an effecter domain that stably contacts the switch II region of the GTPase domain. The domain organization of IF2 is inconsistent with the "articulated lever" mechanism of communication between the GTPase and initiator tRNA binding domains that has been proposed for eIF5B. Previous cryo-electron microscopy reconstructions, NMR experiments, and this structure show that IF2 transitions from being flexible in solution to an extended conformation when interacting with ribosomal complexes.

  • Organizational Affiliation

    Departments of Chemistry and Molecular Biochemistry and Biophysics, Yale University, New Haven, CT 06520.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor IF-2A,
B [auth D],
C [auth B],
D [auth C]
473Thermus thermophilus HB8Mutation(s): 1 
Gene Names: infBTTHA0699
Find proteins for P48515 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore P48515 
Go to UniProtKB:  P48515
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48515
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.83α = 90
b = 177.816β = 89.87
c = 61.793γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-11
    Type: Initial release
  • Version 1.1: 2013-09-25
    Changes: Database references
  • Version 1.2: 2013-10-09
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description