Crystal Structure of Translation Initiation Factor 5A from Pyrococcus Horikoshii

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.185 

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Crystal Structure of Hyperthermophilic Archaeal Initiation Factor 5A: A Homologue of Eukaryotic Initiation Factor 5A (eIF-5A)

Yao, M.Ohsawa, A.Kikukawa, S.Tanaka, I.Kimura, M.

(2003) J Biochem 133: 75-81

  • DOI: https://doi.org/10.1093/jb/mvg011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Eukaryotic initiation factor 5A (eIF-5A) is ubiquitous in eukaryotes and archaebacteria and is essential for cell proliferation and survival. The crystal structure of the eIF-5A homologue (PhoIF-5A) from a hyperthermophilic archaebacterium Pyrococcus horikoshii OT3 was determined at 2.0 A resolution by the molecular replacement method. PhoIF-5A is predominantly composed of beta-strands comprising two distinct folding domains, an N-domain (residues 1-69) and a C-domain (residues 72-138), connected by a short linker peptide (residues 70-71). The N-domain has an SH3-like barrel, while the C-domain folds in an (oligonucleotide/oligosaccharide binding) OB fold. Comparison of the structure of PhoIF-5A with those of archaeal homologues from Methanococcus jannaschii and Pyrobaculum aerophilum showed that the N-domains could be superimposed with root mean square deviation (rmsd) values of 0.679 and 0.624 A, while the C-domains gave higher values of 1.824 and 1.329 A, respectively. Several lines of evidence suggest that eIF-5A functions as a biomodular protein capable of interacting with protein and nucleic acid. The surface representation of electrostatic potential shows that PhoIF-5A has a concave surface with positively charged residues between the N- and C-domains. In addition, a flexible long hairpin loop, L1 (residues 33-41), with a hypusine modification site is positively charged, protruding from the N-domain. In contrast, the opposite side of the concave surface at the C-domain is mostly negatively charged. These findings led to the speculation that the concave surface and loop L1 at the N-domain may be involved in RNA binding, while the opposite side of the concave surface in the C-domain may be involved in protein interaction.

  • Organizational Affiliation

    Division of Biological Science, Graduate School of Science, Hokkaido University, Sapporo 066-0810.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Initiation Factor 5A
A, B, C
138Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: PH1381
Find proteins for O50089 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O50089 
Go to UniProtKB:  O50089
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50089
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.185 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.28α = 90
b = 93.28β = 90
c = 39.43γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Refinement description