PDBsum entry 4z9k

Hydrolase/immune system

PDB id: 4z9k

Contents

Protein chains

258 a.a.

116 a.a.

Ligands

EDO ×2

Metals

_CL ×2

_ZN

Waters ×330

PDB id:

4z9k

Name:

Hydrolase/immune system

Title:

Ricin a chain bound to camelid nanobody (vhh2)(f5)

Structure:

Ricin. Chain: a. Fragment: unp residues 39-296. Engineered: yes. Vhh2(f5) antibody. Chain: b. Engineered: yes

Source:

Ricinus communis. Castor bean. Organism_taxid: 3988. Expressed in: escherichia coli. Expression_system_taxid: 469008. Vicugna pacos. Alpaca. Organism_taxid: 30538. Expression_system_taxid: 562

Resolution:

1.50Å R-factor: 0.179 R-free: 0.195

Authors:

M.J.Rudolph

Key ref:

M.J.Rudolph et al. (2016). Structural analysis of nested neutralizing and non-neutralizing B cell epitopes on ricin toxin's enzymatic subunit. Proteins, 84, 1162-1172. PubMed id: 27159829

Date:

10-Apr-15 Release date: 20-Jul-16

Protein chain

P02879  (RICI_RICCO) -  Ricin from Ricinus communis

Seq: 576 a.a.

Struc: 258 a.a.

Protein chain

No UniProt id for this chain

Struc: 116 a.a.

Enzyme reactions

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

Proteins 84:1162-1172 (2016)

PubMed id: 27159829

Structural analysis of nested neutralizing and non-neutralizing B cell epitopes on ricin toxin's enzymatic subunit.

M.J.Rudolph, D.J.Vance, M.S.Cassidy, Y.Rong, C.B.Shoemaker, N.J.Mantis.

ABSTRACT

In this report, we describe the X-ray crystal structures of two single domain camelid antibodies (VH H), F5 and F8, each in complex with ricin toxin's enzymatic subunit (RTA). F5 has potent toxin-neutralizing activity, while F8 has weak neutralizing activity. F5 buried a total of 1760 Å(2) in complex with RTA and made contact with three prominent secondary structural elements: α-helix B (Residues 98-106), β-strand h (Residues 113-117), and the C-terminus of α-helix D (Residues 154-156). F8 buried 1103 Å(2) in complex with RTA that was centered primarily on β-strand h. As such, the structural epitope of F8 is essentially nested within that of F5. All three of the F5 complementarity determining regions CDRs were involved in RTA contact, whereas F8 interactions were almost entirely mediated by CDR3, which essentially formed a seventh β-strand within RTA's centrally located β-sheet. A comparison of the two structures reported here to several previously reported (RTA-VH H) structures identifies putative contact sites on RTA, particularly α-helix B, associated with potent toxin-neutralizing activity. This information has implications for rational design of RTA-based subunit vaccines for biodefense. Proteins 2016; 84:1162-1172. © 2016 Wiley Periodicals, Inc.