6RIM | pdb_00006rim

Crystal structure of the catalytic domain of the Weissela oryzae botulinum like toxin

PDB DOI: https://doi.org/10.2210/pdb6RIM/pdb

Classification: TOXIN
Organism(s): Weissella oryzae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-04-24 Released: 2019-05-29
Deposition Author(s): Kosenina, S., Masuyer, G., Stenmark, P.
Funding Organization(s): Swedish Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.202 (Depositor), 0.206 (DCC)
R-Value Work:
0.151 (Depositor), 0.156 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the catalytic domain of the Weissella oryzae botulinum-like toxin.

Kosenina, S., Masuyer, G., Zhang, S., Dong, M., Stenmark, P.

(2019) FEBS Lett 593: 1403-1410

PubMed: 31111466 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.13446
Primary Citation Related Structures:
6RIM

PubMed Abstract:
Botulinum neurotoxins (BoNTs) are the most potent toxins known. So far, eight serotypes have been identified that all act as zinc-dependent endopeptidases targeting SNARE proteins and inhibiting the release of neurotransmitters. Recently, the first botulinum toxin-like protein was identified outside the Clostridial genus, designated BoNT/Wo in the genome of Weissella oryzae. Here, we report the 1.6 Å X-ray crystal structure of the light chain of BoNT/Wo (LC/Wo). LC/Wo presents the core fold common to BoNTs but has an unusually wide, open and negatively charged catalytic pocket, with an additional Ca ²⁺ ion besides the zinc ion and a unique ß-hairpin motif. The structural information will help establish the substrate profile of BoNT/Wo and help our understanding of how BoNT evolved.

Organizational Affiliation

Department of Biochemistry and Biophysics, Stockholm University, Sweden.

Macromolecule Content

Total Structure Weight: 459.21 kDa
Atom Count: 32,682
Modeled Residue Count: 3,586
Deposited Residue Count: 3,984
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative botulinum-like toxin Wo	A, B, C, D, E A, B, C, D, E, F, G, H	498	Weissella oryzae	Mutation(s): 0 Gene Names: WOSG25_110680 EC: 3.4.24.69
UniProt
Find proteins for A0A069CUU9 (Weissella oryzae (strain DSM 25784 / JCM 18191 / LMG 30913 / SG25)) Explore A0A069CUU9 Go to UniProtKB: A0A069CUU9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A069CUU9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain W [auth H] SDF format, chain U [auth G] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain W [auth H] MOL2 format, chain U [auth G] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain W [auth H] mmCIF format, chain U [auth G] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain X [auth H] SDF format, chain V [auth G] SDF format, chain T [auth F] SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] MOL2 format, chain X [auth H] MOL2 format, chain V [auth G] MOL2 format, chain T [auth F] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] mmCIF format, chain X [auth H] mmCIF format, chain V [auth G] mmCIF format, chain T [auth F] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.202 (Depositor), 0.206 (DCC)
R-Value Work: 0.151 (Depositor), 0.156 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.908	α = 101.71
b = 105.208	β = 90
c = 179.621	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-05-29

Deposition Author(s):

Kosenina, S.

Masuyer, G.

Stenmark, P.

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2018-03406

Revision History (Full details and data files)

Version 1.0: 2019-05-29
Type: Initial release
Version 1.1: 2019-06-05
Changes: Data collection, Derived calculations
Version 1.2: 2019-07-03
Changes: Data collection, Database references
Version 1.3: 2019-08-21
Changes: Data collection
Version 1.4: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Structure summary