4U6H

Vaccinia L1/M12B9-Fab complex

  • Classification: IMMUNE SYSTEM
  • Organism(s): Mus musculus, Vaccinia virus WR
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2014-07-29 Released: 2014-08-06 
  • Deposition Author(s): Matho, M.H., Schlossman, A., Zajonc, D.M.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Potent neutralization of vaccinia virus by divergent murine antibodies targeting a common site of vulnerability in l1 protein.

Kaever, T.Meng, X.Matho, M.H.Schlossman, A.Li, S.Sela-Culang, I.Ofran, Y.Buller, M.Crump, R.W.Parker, S.Frazier, A.Crotty, S.Zajonc, D.M.Peters, B.Xiang, Y.

(2014) J Virol 88: 11339-11355

  • DOI: 10.1128/JVI.01491-14
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Vaccinia virus (VACV) L1 is an important target for viral neutralization and has been included in multicomponent DNA or protein vaccines against orthopoxviruses. To further understand the protective mechanism of the anti-L1 antibodies, we generated f ...

    Vaccinia virus (VACV) L1 is an important target for viral neutralization and has been included in multicomponent DNA or protein vaccines against orthopoxviruses. To further understand the protective mechanism of the anti-L1 antibodies, we generated five murine anti-L1 monoclonal antibodies (MAbs), which clustered into 3 distinct epitope groups. While two groups of anti-L1 failed to neutralize, one group of 3 MAbs potently neutralized VACV in an isotype- and complement-independent manner. This is in contrast to neutralizing antibodies against major VACV envelope proteins, such as H3, D8, or A27, which failed to completely neutralize VACV unless the antibodies are of complement-fixing isotypes and complement is present. Compared to nonneutralizing anti-L1 MAbs, the neutralization antibodies bound to the recombinant L1 protein with a significantly higher affinity and also could bind to virions. By using a variety of techniques, including the isolation of neutralization escape mutants, hydrogen/deuterium exchange mass spectrometry, and X-ray crystallography, the epitope of the neutralizing antibodies was mapped to a conformational epitope with Asp35 as the key residue. This epitope is similar to the epitope of 7D11, a previously described potent VACV neutralizing antibody. The epitope was recognized mainly by CDR1 and CDR2 of the heavy chain, which are highly conserved among antibodies recognizing the epitope. These antibodies, however, had divergent light-chain and heavy-chain CDR3 sequences. Our study demonstrates that the conformational L1 epitope with Asp35 is a common site of vulnerability for potent neutralization by a divergent group of antibodies.


    Organizational Affiliation

    Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA xiangy@uthscsa.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Light chain of murine anti-vaccinia L1 IgG2a antibody M12B9B, D219Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of murine anti-vaccinia L1 IgG2a antibody M12B9A, C219Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein L1E, J184Vaccinia virus WRMutation(s): 0 
Gene Names: VACWR088L1R
Find proteins for P07612 (Vaccinia virus (strain Western Reserve))
Explore P07612 
Go to UniProtKB:  P07612
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.829α = 90
b = 102.829β = 90
c = 238.355γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272200900048C
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesP41GM103393

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence