5FG3

Crystal structure of GDP-bound aIF5B from Aeropyrum pernix

• PDB DOI: https://doi.org/10.2210/pdb5FG3/pdb

• Classification: TRANSLATION
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-20 Released: 2016-05-04 
• Deposition Author(s): Murakami, R., Miyoshi, T., Uchiumi, T., Ito, K.
• Funding Organization(s): Japan Society for The Promotion of Science, Uchida Energy Science Promotion Foundation, The Ministry of Education,Culture,Sports,Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.243 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

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

• PubMed: 26868175 
• DOI: https://doi.org/10.1002/prot.25009
• Primary Citation of Related Structures:  
  5FG3


• 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, 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.

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Organizational Affiliation: 

Department of Food and Life Sciences, Graduate School of Science and Technology, Niigata University, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 69.9 kDa 
• Atom Count: 4,996 
• Modelled Residue Count: 598 
• Deposited Residue Count: 623 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable translation initiation factor IF-2	A	623	Aeropyrum pernix K1	Mutation(s): 0  Gene Names: infB, APE_2374
UniProt
Find proteins for Q9Y9B3 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9Y9B3  Go to UniProtKB:  Q9Y9B3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.243 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.853	α = 90
b = 97.448	β = 94.77
c = 61.296	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data collection
MOLREP	phasing
XDS	data reduction
XSCALE	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Murakami, R., Miyoshi, T., Uchiumi, T., Ito, K.

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Funding Organization	Location	Grant Number
Japan Society for The Promotion of Science	Japan	15J04972
Japan Society for The Promotion of Science	Japan	21770108
Uchida Energy Science Promotion Foundation	Japan	22-1-10
The Ministry of Education,Culture,Sports,Science and Technology	Japan	24370073

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description