9PHA | pdb_00009pha

CryoEM structure of the YonE portal protein from Bacillus phage SPbeta

PDB DOI: https://doi.org/10.2210/pdb9PHA/pdb
EM Map EMD-71643: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Spbetavirus SPbeta
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-07-09 Released: 2025-12-31
Deposition Author(s): Mishra, B.P., Ve, T.
Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Molecular characterisation of the Bacillus subtilis SpbK antiphage defence system

Mishra, B.P., Ve, T.

To be published.

Macromolecule Content

Total Structure Weight: 666.34 kDa
Atom Count: 30,144
Modeled Residue Count: 3,600
Deposited Residue Count: 5,820
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPbeta prophage-derived uncharacterized protein YonE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	485	Spbetavirus SPbeta	Mutation(s): 0 Gene Names: yonE, BSU21120
UniProt
Find proteins for O31953 (Bacillus subtilis (strain 168)) Explore O31953 Go to UniProtKB: O31953
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O31953
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	FT200100572
National Health and Medical Research Council (NHMRC, Australia)	Australia	1196590

Revision History (Full details and data files)

Version 1.0: 2025-12-31
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.