7XF2 | pdb_00007xf2

Cry-EM structure of vp51 in white spot syndrome virus capsid

PDB DOI: https://doi.org/10.2210/pdb7XF2/pdb
EM Map EMD-33168: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Whispovirus xiabaidian
Mutation(s): No

Deposited: 2022-03-31 Released: 2023-04-05
Deposition Author(s): Shan, H., Shen, Q.T.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.73 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7XF2

This is version 1.2 of the entry. See complete history.

Literature

structure of vp51 in white spot syndrome virus capsid

Hong, S., Shen, Q.T.

To be published.

Macromolecule Content

Total Structure Weight: 103.93 kDa
Atom Count: 6,591
Modeled Residue Count: 840
Deposited Residue Count: 932
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B	466	Whispovirus xiabaidian	Mutation(s): 0
UniProt
Find proteins for K7WK08 (White spot syndrome virus) Explore K7WK08 Go to UniProtKB: K7WK08
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K7WK08
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.73 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870743

Revision History (Full details and data files)

Version 1.0: 2023-04-05
Type: Initial release
Version 1.1: 2024-07-03
Changes: Data collection
Version 1.2: 2025-07-02
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.