4HR1 | pdb_00004hr1

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.280 (Depositor), 0.277 (DCC)
R-Value Work:
0.232 (Depositor)
R-Value Observed:
0.234 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1155/2013/568053
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 A0ACD6B8E2 (Pyrococcus abyssi virus 1) Explore A0ACD6B8E2 Go to UniProtKB: A0ACD6B8E2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8E2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 A0ACD6B8E2 (Pyrococcus abyssi virus 1) Explore A0ACD6B8E2 Go to UniProtKB: A0ACD6B8E2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8E2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.277 (DCC)
R-Value Work: 0.232 (Depositor)
R-Value Observed: 0.234 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2013-06-19

Deposition Author(s):

Leulliot, N.

Quevillon-Cheruel, S.

Revision History (Full details and data files)

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