8EU5 | pdb_00008eu5

Acheta domesticus segmented densovirus high buoyancy fraction 2 empty capsid structure

PDB DOI: https://doi.org/10.2210/pdb8EU5/pdb
EM Map EMD-28604: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): Solenopsis invicta-associated densovirus
Expression System: Acheta domesticus
Mutation(s): No

Deposited: 2022-10-18 Released: 2022-11-09
Deposition Author(s): Penzes, J.J., McKenna, R., Tijssen, P.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director, National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8EU5

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

Literature

Structural and molecular biology of Acheta domesticus segmented densovirus, the first parvovirus to harbor a bipartite genome

Penzes, J.J., Pham, H.T., Chipman, P., Smith, E., McKenna, R., Tijssen, P.

To be published.

Macromolecule Content

Total Structure Weight: 36.29 kDa
Atom Count: 2,551
Modeled Residue Count: 318
Deposited Residue Count: 318
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A	318	Solenopsis invicta-associated densovirus	Mutation(s): 0 Gene Names: CP
UniProt
Find proteins for A0A891H5C3 (Solenopsis invicta-associated densovirus) Explore A0A891H5C3 Go to UniProtKB: A0A891H5C3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A891H5C3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	0.8.9.3
MODEL REFINEMENT	PHENIX	1.10.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM082946
National Institutes of Health/Office of the Director	United States	OD018142
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	RR025080

Revision History (Full details and data files)

Version 1.0: 2022-11-09
Type: Initial release
Version 1.1: 2023-06-14
Changes: Source and taxonomy
Version 1.2: 2024-06-19
Changes: Data collection, Derived calculations

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.