6OCD | pdb_00006ocd

Ricin A chain bound to VHH antibody V6D4

• PDB DOI: https://doi.org/10.2210/pdb6OCD/pdb

• Classification: TOXIN
• Organism(s): Ricinus communis, Vicugna pacos
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-22 Released: 2020-04-01 
• Deposition Author(s): Rudolph, M.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.228 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Intracellular Neutralization of Ricin Toxin by Single-domain Antibodies Targeting the Active Site.

Rudolph, M.J., Czajka, T.F., Davis, S.A., Thi Nguyen, C.M., Li, X.P., Tumer, N.E., Vance, D.J., Mantis, N.J.

(2020) J Mol Biology 432: 1109-1125

• PubMed: 31931008 
• DOI: https://doi.org/10.1016/j.jmb.2020.01.006
• Primary Citation Related Structures: 
  6OBC, 6OBE, 6OBG, 6OBM, 6OBO, 6OCA, 6OCD


• PubMed Abstract: 
  

  The extreme potency of the plant toxin, ricin, is due to its enzymatic subunit, RTA, which inactivates mammalian ribosomes with near-perfect efficiency. Here we characterized, at the functional and structural levels, seven alpaca single-domain antibodies (V _H Hs) previously reported to recognize epitopes in proximity to RTA's active site. Three of the V _H Hs, V2A11, V8E6, and V2G10, were potent inhibitors of RTA in vitro and protected Vero cells from ricin when expressed as intracellular antibodies ("intrabodies"). Crystal structure analysis revealed that the complementarity-determining region 3 (CDR3) elements of V2A11 and V8E6 penetrate RTA's active site and interact with key catalytic residues. V2G10, by contrast, sits atop the enzymatic pocket and occludes substrate accessibility. The other four V _H Hs also penetrated/occluded RTA's active site, but lacked sufficient binding affinities to outcompete RTA-ribosome interactions. Intracellular delivery of high-affinity, single-domain antibodies may offer a new avenue in the development of countermeasures against ricin toxin.toxin, antibody, structure, intracellular.

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Organizational Affiliation: 
• New York Structural Biology Center, New York, NY 10027, United States. Electronic address: [e-mail].
Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, 12208, United States; Department of Biomedical Sciences, University at Albany, Albany, NY 12201, United States.
New York Structural Biology Center, New York, NY 10027, United States.
Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, United States.
Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, 12208, United States.
Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, 12208, United States; Department of Biomedical Sciences, University at Albany, Albany, NY 12201, United States. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 84.94 kDa 
• Atom Count: 6,243 
• Modeled Residue Count: 750 
• Deposited Residue Count: 762 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin A chain	A, C	258	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH antibody V6D4	B, D	123	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	G [auth A], K [auth C]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	E [auth A], I [auth C], J [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	H [auth A], L [auth C], M [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.228 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.937	α = 90
b = 78.605	β = 96.46
c = 103.89	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Rudolph, M.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201400021C

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2020-10-14
  Changes: Database references, Derived calculations
• Version 1.2: 2024-11-20
  Changes: Advisory, Data collection, Database references, Structure summary