8FBE

Crystal structure of OrfX1 from Clostridium botulinum E1

PDB DOI: https://doi.org/10.2210/pdb8FBE/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Clostridium botulinum E1 str. 'BoNT E Beluga
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-11-29 Released: 2022-12-21
Deposition Author(s): Liu, S., Gao, L.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.216
R-Value Work: 0.172
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structures of OrfX1, OrfX2 and the OrfX1-OrfX3 complex from the orfX gene cluster of botulinum neurotoxin E1.

Gao, L., Lam, K.H., Liu, S., Przykopanski, A., Lubke, J., Qi, R., Kruger, M., Nowakowska, M.B., Selby, K., Douillard, F.P., Dorner, M.B., Perry, K., Lindstrom, M., Dorner, B.G., Rummel, A., Jin, R.

(2023) FEBS Lett 597: 524-537

PubMed: 36653893 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/1873-3468.14576
Primary Citation of Related Structures:
8FBD, 8FBE, 8FBF

PubMed Abstract:
Botulinum neurotoxins (BoNTs) are among the most lethal toxins known to humans, comprising seven established serotypes termed BoNT/A-G encoded in two types of gene clusters (ha and orfX) in BoNT-producing clostridia. The ha cluster encodes four non-toxic neurotoxin-associated proteins (NAPs) that assemble with BoNTs to protect and enhance their oral toxicity. However, the structure and function of the orfX-type NAPs remain largely unknown. Here, we report the crystal structures for OrfX1, OrfX2, and an OrfX1-OrfX3 complex, which are encoded in the orfX cluster of a BoNT/E1-producing Clostridium botulinum strain associated with human foodborne botulism. These structures lay the foundation for future studies on the potential roles of OrfX proteins in oral intoxication and pathogenesis of BoNTs.

Organizational Affiliation

Department of Physiology and Biophysics, University of California, Irvine, CA, USA.

Macromolecule Content

Total Structure Weight: 33.56 kDa
Atom Count: 2,617
Modelled Residue Count: 288
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurotoxin complex component Orf-X1	A, B	144	Clostridium botulinum E1 str. 'BoNT E Beluga	Mutation(s): 1
UniProt
Find proteins for O52975 (Clostridium botulinum) Explore O52975 Go to UniProtKB: O52975
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O52975
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.216
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.602	α = 90
b = 56.602	β = 90
c = 84.299	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-12-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5R01AI091823-05

Revision History (Full details and data files)

Version 1.0: 2022-12-21
Type: Initial release
Version 1.1: 2023-02-08
Changes: Database references
Version 1.2: 2023-03-08
Changes: Database references

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 R01GM133198.