7KBK

Ricin bound to VHH antibody V6E11

Summary for 7KBK

• Entry DOI: 10.2210/pdb7kbk/pdb
• Descriptor: Ricin, VHH antibody V6E11, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... (9 entities in total)
• Functional Keywords: ribosome inactivating protein, vhh antibody, toxin
• Biological source: Vicugna pacos; More
• Total number of polymer chains: 3
• Total formula weight: 76141.91

Authors

Rudolph, M.J. (deposition date: 2020-10-02, release date: 2021-08-04, Last modification date: 2023-10-18)

Primary citation

Rudolph, M.J.,Poon, A.Y.,Kavaliauskiene, S.,Myrann, A.G.,Reynolds-Peterson, C.,Davis, S.A.,Sandvig, K.,Vance, D.J.,Mantis, N.J.
Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies that Bridge Ricin's A-B Subunit Interface.
J.Mol.Biol., 433:167086-167086, 2021

PubMed Abstract: 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 (VHs) that span the RTA-RTB interface, including four Tier 1 VHs with IC values <1 nM. Crystal structures of each VH 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). VHs 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 VHs 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.

PubMed: 34089718
DOI: 10.1016/j.jmb.2021.167086

Experimental method

X-RAY DIFFRACTION (2.091 Å)