4ETQ

Vaccinia virus D8L IMV envelope protein in complex with Fab of murine IgG2a LA5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Biochemical Characterization of the Vaccinia Virus Envelope Protein D8 and Its Recognition by the Antibody LA5.

Matho, M.H.Maybeno, M.Benhnia, M.R.Becker, D.Meng, X.Xiang, Y.Crotty, S.Peters, B.Zajonc, D.M.

(2012) J Virol 86: 8050-8058

  • DOI: 10.1128/JVI.00836-12
  • Primary Citation of Related Structures:  
    4E9O, 4EBQ, 4ETQ

  • PubMed Abstract: 
  • Smallpox vaccine is considered a gold standard of vaccines, as it is the only one that has led to the complete eradication of an infectious disease from the human population. B cell responses are critical for the protective immunity induced by the vaccine, yet their targeted epitopes recognized in humans remain poorly described ...

    Smallpox vaccine is considered a gold standard of vaccines, as it is the only one that has led to the complete eradication of an infectious disease from the human population. B cell responses are critical for the protective immunity induced by the vaccine, yet their targeted epitopes recognized in humans remain poorly described. Here we describe the biochemical and structural characterization of one of the immunodominant vaccinia virus (VACV) antigens, D8, and its binding to the monoclonal antibody LA5, which is capable of neutralizing VACV in the presence of complement. The full-length D8 ectodomain was found to form a tetramer. We determined the crystal structure of the LA5 Fab-monomeric D8 complex at a resolution of 2.1 Å, as well as the unliganded structures of D8 and LA5-Fab at resolutions of 1.42 Å and 1.6 Å, respectively. D8 features a carbonic anhydrase (CAH) fold that has evolved to bind to the glycosaminoglycan (GAG) chondroitin sulfate (CS) on host cells. The central positively charged crevice of D8 was predicted to be the CS binding site by automated docking experiments. Furthermore, sequence alignment of various poxvirus D8 orthologs revealed that this crevice is structurally conserved. The D8 epitope is formed by 23 discontinuous residues that are spread across 80% of the D8 protein sequence. Interestingly, LA5 binds with a high-affinity lock-and-key mechanism above this crevice with an unusually large antibody-antigen interface, burying 2,434 Å(2) of protein surface.


    Organizational Affiliation

    Division of Cell Biology, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, heavy chainC [auth A], A [auth H]221Mus musculusMutation(s): 0 
Gene Names: IgG2aIGHV1S127*01
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
anti-vaccinia D8L antigen murine monoclonal IgG2a antibody LA5, light chainD [auth B], B [auth L]212Mus musculusMutation(s): 0 
Gene Names: IgG2aIGKV4-55*01 germ line
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
IMV membrane proteinF [auth C], E [auth X]269Vaccinia virusMutation(s): 0 
Gene Names: D8LVACAC2_124VACCL3_124VAC_DPP17_124VACV_VK12_RKI-146VACV_VK01_RKI-140VACV_VK02_RKI-117VACV_VK08_RKI-133synVACV_124VACli_124
UniProt
Find proteins for Q1M1K6 (Vaccinia virus)
Explore Q1M1K6 
Go to UniProtKB:  Q1M1K6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.021α = 90
b = 91.156β = 107.32
c = 103.774γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references