6UC6

Crystal structure of BoNT/B receptor-binding domain in complex with VHH JLI-H11

• PDB DOI: https://doi.org/10.2210/pdb6UC6/pdb

• Classification: HYDROLASE/ANTITOXIN
• Organism(s): Clostridium botulinum, Vicugna pacos
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-15 Released: 2020-03-04 
• Deposition Author(s): Lam, K., Jin, R.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.222 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 

Starting Model: experimental

Literature

Structural Insights into Rational Design of Single-Domain Antibody-Based Antitoxins against Botulinum Neurotoxins

Lam, K., Tremblay, J.M., Vazquez-Cintron, E., Perry, K., Ondeck, C., Webb, R., McNutt, P.M., Shoemaker, C.B., Jin, R.

(2020) Cell Rep 30: 2526

• DOI: https://doi.org/10.1016/j.celrep.2020.01.107

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 138.13 kDa 
• Atom Count: 9,263 
• Modelled Residue Count: 1,080 
• Deposited Residue Count: 1,184 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Botulinum neurotoxin type B	A, C [auth B]	438	Clostridium botulinum	Mutation(s): 0  Gene Names: botB EC: 3.4.24.69
UniProt
Find proteins for P10844 (Clostridium botulinum) Explore P10844  Go to UniProtKB:  P10844

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
JLI-H11	B [auth C], D	154	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.222 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.21	α = 87.833
b = 73.276	β = 65.745
c = 76.367	γ = 66.551

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	model building
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Lam, K., Jin, R.

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

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary