6THY | pdb_00006thy

Botulinum neurotoxin A3 Hc domain in complex with GD1a

PDB DOI: https://doi.org/10.2210/pdb6THY/pdb

Classification: TOXIN
Organism(s): Clostridium botulinum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-11-21 Released: 2020-01-29
Deposition Author(s): Gregory, K.S., Acharya, K.R., Liu, S.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.213 (Depositor), 0.205 (DCC)
R-Value Work:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of botulinum neurotoxin subtype A3 cell binding domain in complex with GD1a co-receptor ganglioside.

Gregory, K.S., Liu, S.M., Acharya, K.R.

(2020) FEBS Open Bio 10: 298-305

PubMed: 31945264 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/2211-5463.12790
Primary Citation Related Structures:
6THY

PubMed Abstract:
Botulinum neurotoxins (BoNTs) are one of the most toxic proteins known to humans. Their molecular structure is comprised of three essential domains-a cell binding domain (H _C ), translocation domain and catalytic domain (light chain) . The H _C domain facilitates the highly specific binding of BoNTs to the neuronal membrane via a dual-receptor complex involving a protein receptor and a ganglioside. Variation in activity/toxicity across subtypes of serotype A has been attributed to changes in protein and ganglioside interactions, and their implications are important in the design of novel BoNT-based therapeutics. Here, we present the structure of BoNT/A3 cell binding domain (H _C /A3) in complex with the ganglioside GD1a at 1.75 Å resolution. The structure revealed that six residues interact with the three outermost monosaccharides of GD1a through several key hydrogen bonding interactions. A detailed comparison of structures of H _C /A3 with H _C /A1 revealed subtle conformational differences at the ganglioside binding site upon carbohydrate binding.

Organizational Affiliation

Department of Biology and Biochemistry, Claverton Down, University of Bath, UK.

Macromolecule Content

Total Structure Weight: 52.14 kDa
Atom Count: 3,931
Modeled Residue Count: 409
Deposited Residue Count: 433
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BoNT/A3	A [auth AAA]	433	Clostridium botulinum	Mutation(s): 0
UniProt
Find proteins for Q3LRX9 (Clostridium botulinum) Explore Q3LRX9 Go to UniProtKB: Q3LRX9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3LRX9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B [auth A]	5		N/A	Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
Glycosylation Resources
GlyTouCan: G03277YI GlyCosmos: G03277YI GlyGen: G03277YI

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA]	G [auth AAA], H [auth AAA]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Focus chain H [auth AAA] Interactions & Density Focus chain G [auth AAA] Focus chain H [auth AAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain D [auth AAA] MOL2 format, chain F [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain F [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA], F [auth AAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain F [auth AAA] Interactions & Density Focus chain D [auth AAA] Focus chain F [auth AAA]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth AAA] Interactions & Density Focus chain E [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.213 (Depositor), 0.205 (DCC)
R-Value Work: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.228	α = 90
b = 73.129	β = 90
c = 140.18	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-01-29

Deposition Author(s):

Gregory, K.S.

Acharya, K.R.

Liu, S.M.

Revision History (Full details and data files)

Version 1.0: 2020-01-29
Type: Initial release
Version 1.1: 2020-03-11
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary