6B9J

Structure of vaccinia virus D8 protein bound to human Fab vv138


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-function characterization of three human antibodies targeting the vaccinia virus adhesion molecule D8.

Matho, M.H.Schlossman, A.Gilchuk, I.M.Miller, G.Mikulski, Z.Hupfer, M.Wang, J.Bitra, A.Meng, X.Xiang, Y.Kaever, T.Doukov, T.Ley, K.Crotty, S.Peters, B.Hsieh-Wilson, L.C.Crowe, J.E.Zajonc, D.M.

(2018) J. Biol. Chem. 293: 390-401

  • DOI: 10.1074/jbc.M117.814541
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Vaccinia virus (VACV) envelope protein D8 is one of three glycosaminoglycan adhesion molecules and binds to the linear polysaccharide chondroitin sulfate (CS). D8 is also a target for neutralizing antibody responses that are elicited by the smallpox ...

    Vaccinia virus (VACV) envelope protein D8 is one of three glycosaminoglycan adhesion molecules and binds to the linear polysaccharide chondroitin sulfate (CS). D8 is also a target for neutralizing antibody responses that are elicited by the smallpox vaccine, which has enabled the first eradication of a human viral pathogen and is a useful model for studying antibody responses. However, to date, VACV epitopes targeted by human antibodies have not been characterized at atomic resolution. Here, we characterized the binding properties of several human anti-D8 antibodies and determined the crystal structures of three VACV-mAb variants, VACV-66, VACV-138, and VACV-304, separately bound to D8. Although all these antibodies bound D8 with high affinity and were moderately neutralizing in the presence of complement, VACV-138 and VACV-304 also fully blocked D8 binding to CS-A, the low affinity ligand for D8. VACV-138 also abrogated D8 binding to the high-affinity ligand CS-E, but we observed residual CS-E binding was observed in the presence of VACV-304. Analysis of the VACV-138- and VACV-304-binding sites along the CS-binding crevice of D8, combined with different efficiencies of blocking D8 adhesion to CS-A and CS-E allowed us to propose that D8 has a high- and low-affinity CS-binding region within its central crevice. The crevice is amenable to protein engineering to further enhance both specificity and affinity of binding to CS-E. Finally, a wild-type D8 tetramer specifically bound to structures within the developing glomeruli of the kidney, which express CS-E. We propose that through structure-based protein engineering, an improved D8 tetramer could be used as a potential diagnostic tool to detect expression of CS-E, which is a possible biomarker for ovarian cancer.


    Organizational Affiliation

    the University of California San Diego, La Jolla, California 92037, and.,Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037.,the Departments of Pediatrics, Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232.,the Stanford Synchrotron Radiation Lightsource, SLAC, Menlo Park, California 94025.,From the Divisions of Cell Biology, dzajonc@lji.org.,the Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium.,the Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California 91126.,the Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, Texas 78229.,From the Divisions of Cell Biology.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IMV membrane protein
X, Y
241Vaccinia virusMutation(s): 0 
Find proteins for Q1M1K6 (Vaccinia virus)
Go to UniProtKB:  Q1M1K6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab vv138 Heavy chain
H, A
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab vv138 Light chain
L, B
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
H, X, Y
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
X, Y
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.241 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 234.282α = 90.00
b = 253.842β = 90.00
c = 73.760γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-10-10 
  • Released Date: 2017-11-22 
  • Deposition Author(s): Zajonc, D.M.
  • This entry supersedes: 5USI

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesHHSN272200900048C

Revision History 

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Author supporting evidence
  • Version 1.2: 2018-01-17
    Type: Database references