5ZCY

Crystal structure of archaeal translation initiation factor 1 at 1.5 Angstroms resolution

• PDB DOI: https://doi.org/10.2210/pdb5ZCY/pdb

• Classification: TRANSLATION
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-22 Released: 2018-05-02 
• Deposition Author(s): Gogoi, P., Kanaujia, S.P.
• Funding Organization(s): Department of Biotechnology Government of India

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.205 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Starting Model: experimental

Literature

Archaeal and eukaryal translation initiation factor 1 differ in their RNA interacting loops.

Gogoi, P., Kanaujia, S.P.

(2018) FEBS Lett 592: 1602-1610

• PubMed: 29608219 
• DOI: https://doi.org/10.1002/1873-3468.13044
• Primary Citation of Related Structures:  
  5ZCY


• PubMed Abstract: 
  

  The archaeal translation initiation factor 1 (aIF1) is reported to be functionally homologous to the eukaryotic translation initiation factor 1 (eIF1). However, lack of a structural comparison between aIF1 and eIF1 has limited our understanding of the structural (dis)similarities. Herein, we have determined the three-dimensional crystal structure of an open reading frame PH1771.1 encoding aIF1 in Pyrococcus horikoshii OT3. Results reveal that although aIF1 has low sequence similarity with eIF1, high structural homology exists between the two proteins. Nonetheless, notable critical differences between aIF1 and eIF1 could still be perceived at the β ₁ -β ₂ basic loop, the acidic loop and the solvent-exposed surface. These differences might lead to a slightly divergent mode of action of aIF1 during archaeal translation initiation.

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Organizational Affiliation: 

Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India.

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: 11.58 kDa 
• Atom Count: 760 
• Modelled Residue Count: 83 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein translation factor SUI1 homolog	A	99	Pyrococcus horikoshii OT3	Mutation(s): 0  Gene Names: PH1771.1
UniProt
Find proteins for P58193 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore P58193  Go to UniProtKB:  P58193

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	B [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
NO2	C [auth A]	NITRITE ION N O2 IOVCWXUNBOPUCH-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.205 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.58	α = 90
b = 53.58	β = 90
c = 56.94	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Gogoi, P., Kanaujia, S.P.

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Funding Organization	Location	Grant Number
Department of Biotechnology Government of India	India	BT/302/NE/TBP/2012

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2018-05-23
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description