1G7T

X-RAY STRUCTURE OF TRANSLATION INITIATION FACTOR IF2/EIF5B COMPLEXED WITH GDPNP

• PDB DOI: https://doi.org/10.2210/pdb1G7T/pdb

• Classification: TRANSLATION
• Organism(s): Methanothermobacter thermautotrophicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-11-14 Released: 2000-12-01 
• Deposition Author(s): Roll-Mecak, A., Cao, C., Dever, T.E., Burley, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.267 
• R-Value Work: 0.231 

Literature

X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding.

Roll-Mecak, A., Cao, C., Dever, T.E., Burley, S.K.

(2000) Cell 103: 781-792

• PubMed: 11114334 
• DOI: https://doi.org/10.1016/s0092-8674(00)00181-1
• Primary Citation of Related Structures:  
  1G7R, 1G7S, 1G7T


• PubMed Abstract: 
  

  X-ray structures of the universal translation initiation factor IF2/eIF5B have been determined in three states: free enzyme, inactive IF2/eIF5B.GDP, and active IF2/eIF5B.GTP. The "chalice-shaped" enzyme is a GTPase that facilitates ribosomal subunit joining and Met-tRNA(i) binding to ribosomes in all three kingdoms of life. The conserved core of IF2/eIF5B consists of an N-terminal G domain (I) plus an EF-Tu-type beta barrel (II), followed by a novel alpha/beta/alpha-sandwich (III) connected via an alpha helix to a second EF-Tu-type beta barrel (IV). Structural comparisons reveal a molecular lever, which amplifies a modest conformational change in the Switch 2 region of the G domain induced by Mg(2+)/GTP binding over a distance of 90 A from the G domain active center to domain IV. Mechanisms of GTPase function and ribosome binding are discussed.

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Organizational Affiliation: 

Laboratories of Molecular Biophysics The Rockefeller University 10021, New York, NY 10021, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.89 kDa 
• Atom Count: 4,734 
• Modelled Residue Count: 569 
• Deposited Residue Count: 594 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSLATION INITIATION FACTOR IF2/EIF5B	A	594	Methanothermobacter thermautotrophicus	Mutation(s): 0
UniProt
Find proteins for O26359 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26359  Go to UniProtKB:  O26359

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.267 
• R-Value Work: 0.231 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.799	α = 105.17
b = 53.68	β = 94.76
c = 94.926	γ = 100.17

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-01 
Deposition Author(s): Roll-Mecak, A., Cao, C., Dever, T.E., Burley, S.K.

Revision History  

• Version 1.0: 2000-12-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations