5FG3

Crystal structure of GDP-bound aIF5B from Aeropyrum pernix


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of translation initiation factor 5B from the crenarchaeon Aeropyrum pernix.

Murakami, R.Miyoshi, T.Uchiumi, T.Ito, K.

(2016) Proteins 84: 712-717

  • DOI: 10.1002/prot.25009

  • PubMed Abstract: 
  • Initiation factor 5B (IF5B) is a universally conserved translational GTPase that catalyzes ribosomal subunit joining. In eukaryotes, IF5B directly interacts via a groove in its domain IV with initiation factor 1A (IF1A), another universally conserved ...

    Initiation factor 5B (IF5B) is a universally conserved translational GTPase that catalyzes ribosomal subunit joining. In eukaryotes, IF5B directly interacts via a groove in its domain IV with initiation factor 1A (IF1A), another universally conserved initiation factor, to accomplish efficient subunit joining. Here, we have determined the first structure of a crenarchaeal IF5B, which revealed that the archaea-specific region of IF5B (helix α15) binds and occludes the groove of domain IV. Therefore, archaeal IF5B cannot access IF1A in the same manner as eukaryotic IF5B. This fact suggests that different relationships between IF5B and IF1A exist in archaea and eukaryotes.


    Organizational Affiliation

    Department of Biology, Faculty of Science, Niigata University, Japan.,Department of Food and Life Sciences, Graduate School of Science and Technology, Niigata University, Japan.,Center for Transdisciplinary Research, Niigata University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable translation initiation factor IF-2
A
623Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)Mutation(s): 0 
Gene Names: infB
Find proteins for Q9Y9B3 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Go to UniProtKB:  Q9Y9B3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.853α = 90.00
b = 97.448β = 94.77
c = 61.296γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XSCALEdata scaling
XDSdata collection
Cootmodel building
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for The Promotion of ScienceJapan15J04972
Japan Society for The Promotion of ScienceJapan21770108
Uchida Energy Science Promotion FoundationJapan22-1-10
The Ministry of Education,Culture,Sports,Science and TechnologyJapan24370073

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release