9S3S | pdb_00009s3s

Capsid structure of Chaetoceros lorenzianus DNA virus (ClorDNAV), a CRESS-DNA bacilladnavirus

PDB DOI: https://doi.org/10.2210/pdb9S3S/pdb
EM Map EMD-54550: EMDB EMDataResource

Classification: VIRUS
Organism(s): Chaetoceros lorenzianus DNA virus
Mutation(s): No

Deposited: 2025-07-25 Released: 2025-08-13
Deposition Author(s): Munke, A., Gebhard, J.
Funding Organization(s): Carl Trygger Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural diversity and conservation among CRESS-DNA bacilladnaviruses revealed through cryo-EM and computational modelling

Gebhard, J., Tomaru, Y., Okamoto, K., Munke, A.

To be published.

Macromolecule Content

Total Structure Weight: 128.84 kDa
Atom Count: 7,866
Modeled Residue Count: 1,027
Deposited Residue Count: 1,170
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein protein	A, B, C	390	Chaetoceros lorenzianus DNA virus	Mutation(s): 0
UniProt
Find proteins for E9RFF1 (Protobacilladnavirus chaelor) Explore E9RFF1 Go to UniProtKB: E9RFF1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E9RFF1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.5.3
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Carl Trygger Foundation	Sweden	23:2665

Revision History (Full details and data files)

Version 1.0: 2025-08-13
Type: Initial release

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.