7YJL | pdb_00007yjl

Melbournevirus major capsid protein built from 4.4A reconstruction

PDB DOI: https://doi.org/10.2210/pdb7YJL/pdb
EM Map EMD-31529: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Marseillevirus sp. 'Melbournevirus
Mutation(s): No

Deposited: 2022-07-20 Released: 2023-08-02
Deposition Author(s): Burton-Smith, R.N., Okamoto, K., Murata, K.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Swedish Research Council, The Swedish Foundation for Strategic Research

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

The 4.4A structure of the giant Melbournevirus virion belonging to the Marseilleviridae family

Burton-Smith, R.N., Reddy, H.K.N., Svenda, M., Abergel, C., Okamoto, K., Murata, K.

To be published.

Macromolecule Content

Total Structure Weight: 50.9 kDa
Atom Count: 3,599
Modeled Residue Count: 459
Deposited Residue Count: 459
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A	459	Marseillevirus sp. 'Melbournevirus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-02

Deposition Author(s):

Burton-Smith, R.N.

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP19H04845
Swedish Research Council	Sweden	2018-03387
The Swedish Foundation for Strategic Research	Sweden	JA2014-5721
Swedish Research Council	Sweden	2018-00421

Revision History (Full details and data files)

Version 1.0: 2023-08-02
Type: Initial release
Version 1.1: 2024-07-03
Changes: Data collection
Version 1.2: 2025-07-02
Changes: Data collection, Structure summary

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.