6O6B | pdb_00006o6b

Rotavirus A-VP3 (RVA-VP3)

PDB DOI: https://doi.org/10.2210/pdb6O6B/pdb
EM Map EMD-0632: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Rotavirus A
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2019-03-05 Released: 2020-03-11
Deposition Author(s): Kumar, D., Yu, X., Prasad, V., Wang, Z.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Welch Foundation, Robert A. Welch Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 6O6B

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

Literature

A sub-atomic resolution cryo-EM of full-length Rotavirus A-VP3 (RVA-VP3)

Kumar, D., Yu, X., Prasad, V., Wang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 392.27 kDa
Atom Count: 27,532
Modeled Residue Count: 3,312
Deposited Residue Count: 3,340
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein VP3	A, B, C, D	835	Rotavirus A	Mutation(s): 0 Gene Names: VP3 EC: 3.1.4 (PDB Primary Data), 2.7.7.50 (PDB Primary Data), 2.1.1.56 (PDB Primary Data)
UniProt
Find proteins for Q1WK45 (Rotavirus A) Explore Q1WK45 Go to UniProtKB: Q1WK45
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1WK45
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GP Query on 5GP Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-03-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI36040
Welch Foundation	United States	Q-1967-20180324
Robert A. Welch Foundation	United States	Q1279

Revision History (Full details and data files)

Version 1.0: 2020-03-11
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references

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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.