1BEV | pdb_00001bev

BOVINE ENTEROVIRUS VG-5-27

PDB DOI: https://doi.org/10.2210/pdb1BEV/pdb

Classification: VIRUS
Organism(s): Bovine enterovirus strain VG-5-27
Expression System: Mesocricetus auratus
Mutation(s): No

Deposited: 1996-04-03 Released: 1998-09-16
Deposition Author(s): Smyth, M., Tate, J., Lyons, C., Hoey, E., Martin, S., Stuart, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Work:
0.225 (Depositor)
R-Value Observed:
0.225 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Implications for viral uncoating from the structure of bovine enterovirus.

Smyth, M., Tate, J., Hoey, E., Lyons, C., Martin, S., Stuart, D.

(1995) Nat Struct Biol 2: 224-231

PubMed: 7773791 Search on PubMed
DOI: https://doi.org/10.1038/nsb0395-224
Primary Citation Related Structures:
1BEV

PubMed Abstract:
We have determined the crystal structure of a bovine enterovirus, revealing that the topologies of the major capsid proteins and the overall architecture of the virion are similar to those of related picornaviruses. The external loops joining beta-strands are truncated and the canyon region is partially filled by an extension of the VP3 G-H loop giving the viral capsid a relatively smooth appearance. These changes may have implications for cell attachment. In spite of these differences the virus maintains a hydrophobic pocket within VP1, occupied by a specific 'pocket factor' which appears to be myristic acid. These observations support the proposal that a kinetic equilibrium exists between occupied and unoccupied pocket states, with occupation inhibiting uncoating.

Organizational Affiliation

Laboratory of Molecular Biophysics, Oxford, UK.

Macromolecule Content

Total Structure Weight: 92.92 kDa
Atom Count: 6,315
Modeled Residue Count: 794
Deposited Residue Count: 839
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4	A [auth 1]	281	Bovine enterovirus strain VG-5-27	Mutation(s): 0
UniProt
Find proteins for P12915 (Bovine enterovirus (strain VG-5-27)) Explore P12915 Go to UniProtKB: P12915
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12915
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4	B [auth 2]	248	Bovine enterovirus strain VG-5-27	Mutation(s): 0
UniProt
Find proteins for P12915 (Bovine enterovirus (strain VG-5-27)) Explore P12915 Go to UniProtKB: P12915
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12915
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4	C [auth 3]	242	Bovine enterovirus strain VG-5-27	Mutation(s): 0
UniProt
Find proteins for P12915 (Bovine enterovirus (strain VG-5-27)) Explore P12915 Go to UniProtKB: P12915
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12915
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BOVINE ENTEROVIRUS COAT PROTEINS VP1 TO VP4	D [auth 4]	68	Bovine enterovirus strain VG-5-27	Mutation(s): 0
UniProt
Find proteins for P12915 (Bovine enterovirus (strain VG-5-27)) Explore P12915 Go to UniProtKB: P12915
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12915
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MYR Query on MYR Download:Ideal Coordinates CCD File SDF format, chain F [auth 1] MOL2 format, chain F [auth 1] mmCIF format, chain F [auth 1]	F [auth 1]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain F [auth 1]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth 1] SDF format, chain G [auth 2] MOL2 format, chain E [auth 1] MOL2 format, chain G [auth 2] mmCIF format, chain E [auth 1] mmCIF format, chain G [auth 2]	E [auth 1], G [auth 2]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth 1] Focus chain G [auth 2]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Work: 0.225 (Depositor)
R-Value Observed: 0.225 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 388.2	α = 90
b = 392.6	β = 112.7
c = 360.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1998-09-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1998-09-16
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations, Other