9B6M | pdb_00009b6m

Cryo-EM structure and molecular assembly of the BoNT-like toxin PG1 complex from Paeniclostridium ghonii

PDB DOI: https://doi.org/10.2210/pdb9B6M/pdb
EM Map EMD-44266: EMDB EMDataResource

Classification: TOXIN
Organism(s): Paraclostridium ghonii
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2024-03-25 Released: 2025-03-26
Deposition Author(s): Yin, L., Dong, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 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

Cryo-EM structure and molecular assembly of the BoNT-like toxin PG1 complex from Paeniclostridium ghonii

Yin, L., Dong, M.

To be published.

Macromolecule Content

Total Structure Weight: 140.28 kDa
Atom Count: 9,803
Modeled Residue Count: 1,220
Deposited Residue Count: 1,230
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PG1 light chain	A	392	Paraclostridium ghonii	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PG1 heavy chain	B	838	Paraclostridium ghonii	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: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2
RECONSTRUCTION	cryoSPARC	4.4.1

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI132387

Revision History (Full details and data files)

Version 1.0: 2025-03-26
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.