7KDM image
Deposition Date 2020-10-08
Release Date 2021-08-04
Last Version Date 2024-11-20
Entry Detail
PDB ID:
7KDM
Keywords:
Title:
Ricin bound to VHH antibody V5G6
Biological Source:
Source Organism:
Lama glama (Taxon ID: 9844)
Ricinus communis (Taxon ID: 3988)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.30 Å
R-Value Free:
0.23
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Ricin chain A
Chain IDs:A, D
Chain Length:267
Number of Molecules:2
Biological Source:Ricinus communis
Polymer Type:polypeptide(L)
Molecule:Ricin chain B
Chain IDs:B, E
Chain Length:262
Number of Molecules:2
Biological Source:Ricinus communis
Polymer Type:polypeptide(L)
Molecule:Anti-RON nanobody
Chain IDs:C, F
Chain Length:130
Number of Molecules:2
Biological Source:Lama glama
Primary Citation
Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies that Bridge Ricin's A-B Subunit Interface.
J.Mol.Biol. 433 167086 167086 (2021)
PMID: 34089718 DOI: 10.1016/j.jmb.2021.167086

Abstact

Ricin toxin kills mammalian cells with notorious efficiency. The toxin's B subunit (RTB) is a Gal/GalNAc-specific lectin that attaches to cell surfaces and promotes retrograde transport of ricin's A subunit (RTA) to the trans Golgi network (TGN) and endoplasmic reticulum (ER). RTA is liberated from RTB in the ER and translocated into the cell cytoplasm, where it functions as a ribosome-inactivating protein. While antibodies against ricin's individual subunits have been reported, we now describe seven alpaca-derived, single-domain antibodies (VHHs) that span the RTA-RTB interface, including four Tier 1 VHHs with IC50 values <1 nM. Crystal structures of each VHH bound to native ricin holotoxin revealed three different binding modes, based on contact with RTA's F-G loop (mode 1), RTB's subdomain 2γ (mode 2) or both (mode 3). VHHs in modes 2 and 3 were highly effective at blocking ricin attachment to HeLa cells and immobilized asialofetuin, due to framework residues (FR3) that occupied the 2γ Gal/GalNAc-binding pocket and mimic ligand. The four Tier 1 VHHs also interfered with intracellular functions of RTB, as they neutralized ricin in a post-attachment cytotoxicity assay (e.g., the toxin was bound to cell surfaces before antibody addition) and reduced the efficiency of toxin transport to the TGN. We conclude that the RTA-RTB interface is a target of potent toxin-neutralizing antibodies that interfere with both extracellular and intracellular events in ricin's cytotoxic pathway.

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Primary Citation of related structures