3G39

Structure of a lamprey variable lymphocyte receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen.

Velikovsky, C.A.Deng, L.Tasumi, S.Iyer, L.M.Kerzic, M.C.Aravind, L.Pancer, Z.Mariuzza, R.A.

(2009) Nat Struct Mol Biol 16: 725-730

  • DOI: 10.1038/nsmb.1619
  • Primary Citation of Related Structures:  
    3G39, 3G3A, 3G3B

  • PubMed Abstract: 
  • Variable lymphocyte receptors (VLRs) are leucine-rich repeat proteins that mediate adaptive immunity in jawless vertebrates. VLRs are fundamentally different from the antibodies of jawed vertebrates, which consist of immunoglobulin (Ig) domains. We determined the structure of an anti-hen egg white lysozyme (HEL) VLR, isolated by yeast display, bound to HEL ...

    Variable lymphocyte receptors (VLRs) are leucine-rich repeat proteins that mediate adaptive immunity in jawless vertebrates. VLRs are fundamentally different from the antibodies of jawed vertebrates, which consist of immunoglobulin (Ig) domains. We determined the structure of an anti-hen egg white lysozyme (HEL) VLR, isolated by yeast display, bound to HEL. The VLR, whose affinity resembles that of IgM antibodies, uses nearly all its concave surface to bind the protein, in addition to a loop that penetrates into the enzyme active site. The VLR-HEL structure combined with sequence analysis revealed an almost perfect match between ligand-contacting positions and positions with highest sequence diversity. Thus, it is likely that we have defined the generalized antigen-binding site of VLRs. We further demonstrated that VLRs can be affinity-matured by 13-fold to affinities as high as those of IgG antibodies, making VLRs potential alternatives to antibodies for biotechnology applications.


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, WM Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, Rockville, Maryland, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Variable lymphocyte receptor VLRB.2D A170Petromyzon marinusMutation(s): 0 
Gene Names: vlr
Find proteins for D0VX17 (Petromyzon marinus)
Explore D0VX17 
Go to UniProtKB:  D0VX17
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.543α = 90
b = 49.543β = 90
c = 97.912γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance