PDBsum entry 6ocd

Toxin

PDB id: 6ocd

Contents

Protein chains

257 a.a.

114 a.a.

121 a.a.

Ligands

IMD ×2

EDO ×3

Metals

_ZN ×3

_CL

Waters ×301

PDB id:

6ocd

Name:

Toxin

Title:

Ricin a chain bound to vhh antibody v6d4

Structure:

Ricin a chain. Chain: a, c. Fragment: toxin catalytic subunit, residues 40-297. Engineered: yes. Vhh antibody v6d4. Chain: b, d. Engineered: yes

Source:

Ricinus communis. Castor bean. Organism_taxid: 3988. Expressed in: escherichia coli. Expression_system_taxid: 562. Vicugna pacos. Alpaca. Organism_taxid: 30538. Expression_system_taxid: 562

Resolution:

2.10Å R-factor: 0.191 R-free: 0.228

Authors:

M.J.Rudolph

Key ref:

M.J.Rudolph et al. (2020). Intracellular Neutralization of Ricin Toxin by Single-domain Antibodies Targeting the Active Site. J Mol Biol, 432, 1109-1125. PubMed id: 31931008 DOI: 10.1016/j.jmb.2020.01.006

Date:

22-Mar-19 Release date: 01-Apr-20

Protein chains

P02879  (RICI_RICCO) -  Ricin from Ricinus communis

Seq: 576 a.a.

Struc: 257 a.a.

Protein chain

No UniProt id for this chain

Struc: 114 a.a.

Protein chain

No UniProt id for this chain

Struc: 121 a.a.

Enzyme reactions

• Enzyme class: Chains A, C: E.C.3.2.2.22 - rRNA N-glycosylase.
• Reaction: Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.

DOI no: 10.1016/j.jmb.2020.01.006

J Mol Biol 432:1109-1125 (2020)

PubMed id: 31931008

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

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

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_HHs) previously reported to recognize epitopes in proximity to RTA's active site. Three of the V_HHs, 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_HHs 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.