4Z9K

Ricin A chain bound to camelid nanobody (VHH2)(F5)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

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

(2016) Proteins 84: 1162-1172

  • DOI: 10.1002/prot.25062
  • Primary Citation of Related Structures:  
    4Z9K, 5E1H

  • PubMed 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 ...

    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.


    Related Citations: 
    • Crystal Structures of Ricin Toxin's Enzymatic Subunit (RTA) in Complex with Neutralizing and Non-Neutralizing Single-Chain Antibodies.
      Rudolph, M.J., Vance, D.J., Cheung, J., Franklin, M.C., Burshteyn, F., Cassidy, M.S., Gary, E.N., Herrera, C., Shoemaker, C.B., Mantis, N.J.
      () To be published --: --

    Organizational Affiliation

    Department of Biomedical Sciences, University at Albany, Albany, New York, 12201.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RicinA258Ricinus communisMutation(s): 0 
EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis)
Explore P02879 
Go to UniProtKB:  P02879
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VHH2(F5) antibodyB116Vicugna pacosMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.376α = 90
b = 107.085β = 90
c = 111.944γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-04-10 
  • Released Date: 2016-07-20 
  • Deposition Author(s): Rudolph, M.J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence