Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.49 kDa 
• Atom Count: 1416 
• Modelled Residue Count: 165 
• Deposited Residue Count: 170 
• Unique protein chains: 1

3G39

Structure of a lamprey variable lymphocyte receptor

• DOI: 10.2210/pdb3G39/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Petromyzon marinus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-02 Released: 2009-06-23 
• Deposition Author(s): Deng, L., Velikovsky, C.A., Mariuzza, R.A.

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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 

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

• PubMed: 19543291 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Variable lymphocyte receptor VLRB.2D	A	170	Petromyzon marinus	Mutation(s): 0  Gene Names: vlr
Find proteins for D0VX17 (Petromyzon marinus) Explore D0VX17  Go to UniProtKB:  D0VX17

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 = 49.543	α = 90
b = 49.543	β = 90
c = 97.912	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-02 
• Released Date: 2009-06-23 
Deposition Author(s): Deng, L., Velikovsky, C.A., Mariuzza, R.A.

Revision History  

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