4HR1

Structure of PAV1-137, a protein from the virus PAV1 that infects Pyrococcus abyssi.

• PDB DOI: https://doi.org/10.2210/pdb4HR1/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Pyrococcus abyssi virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-26 Released: 2013-06-19 
• Deposition Author(s): Leulliot, N., Quevillon-Cheruel, S., Graille, M., Geslin, C., Flament, D., Romancer, M.L., Tilbeurgh, H.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.280 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Literature

Crystal structure of PAV1-137: a protein from the virus PAV1 that infects Pyrococcus abyssi

Leulliot, N., Quevillon-Cheruel, S., Graille, M., Geslin, C., Flament, D., Romancer, M.L., Tilbeurgh, H.V.

(2013) Archaea 2013: 568053-568053

• PubMed: 23533329 
• DOI: https://doi.org/10.1155/2013/568053
• Primary Citation of Related Structures:  
  4HR1


• PubMed Abstract: 
  

  Pyrococcus abyssi virus 1 (PAV1) was the first virus particle infecting a hyperthermophilic Euryarchaeota (Pyrococcus abyssi strain GE23) that has been isolated and characterized. It is lemon shaped and is decorated with a short fibered tail. PAV1 morphologically resembles the fusiform members of the family Fuselloviridae or the genus Salterprovirus. The 18 kb dsDNA genome of PAV1 contains 25 predicted genes, most of them of unknown function. To help assigning functions to these proteins, we have initiated structural studies of the PAV1 proteome. We determined the crystal structure of a putative protein of 137 residues (PAV1-137) at a resolution of 2.2 Å. The protein forms dimers both in solution and in the crystal. The fold of PAV1-137 is a four- α -helical bundle analogous to those found in some eukaryotic adhesion proteins such as focal adhesion kinase, suggesting that PAV1-137 is involved in protein-protein interactions.

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Organizational Affiliation: 

Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, CNRS-UMR 8619, IFR115, Université Paris-Sud, Bâtiment 430, 91405 Orsay, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 28.98 kDa 
• Atom Count: 1,914 
• Modelled Residue Count: 237 
• Deposited Residue Count: 252 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	126	Pyrococcus abyssi virus 1	Mutation(s): 0  Gene Names: ORF137, Pav1-137
UniProt
Find proteins for A5Y2E1 (Pyrococcus abyssi virus 1) Explore A5Y2E1  Go to UniProtKB:  A5Y2E1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	B	126	Pyrococcus abyssi virus 1	Mutation(s): 0  Gene Names: ORF137
UniProt
Find proteins for A5Y2E1 (Pyrococcus abyssi virus 1) Explore A5Y2E1  Go to UniProtKB:  A5Y2E1

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.280 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.5458	α = 90
b = 73.5458	β = 90
c = 191.5493	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SHARP	phasing
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
Deposition Author(s): Leulliot, N., Quevillon-Cheruel, S., Graille, M., Geslin, C., Flament, D., Romancer, M.L., Tilbeurgh, H.V.

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary