1XT5

Crystal Structure of VCBP3, domain 1, from Branchiostoma floridae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ancient evolutionary origin of diversified variable regions demonstrated by crystal structures of an immune-type receptor in amphioxus.

Haire, R.N.Allaire, M.Jakoncic, J.Stojanoff, V.Cannon, J.P.Litman, G.W.Ostrov, D.A.

(2006) Nat.Immunol. 7: 875-882

  • DOI: 10.1038/ni1359
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Although the origins of genes encoding the rearranging binding receptors remain obscure, it is predicted that their ancestral forms were nonrearranging immunoglobulin-type domains. Variable region-containing chitin-binding proteins (VCBPs) are divers ...

    Although the origins of genes encoding the rearranging binding receptors remain obscure, it is predicted that their ancestral forms were nonrearranging immunoglobulin-type domains. Variable region-containing chitin-binding proteins (VCBPs) are diversified immune-type molecules found in amphioxus (Branchiostoma floridae), an invertebrate that diverged early in deuterostome phylogeny. To study the potential evolutionary relationships between VCBPs and vertebrate adaptive immune receptors, we solved the structures of both a single V-type domain (to 1.15 A) and a pair of V-type domains (to 1.85 A) from VCBP3. The deduced structures show integral features of the ancestral variable-region fold as well as unique features of variable-region pairing in molecules that may reflect characteristics of ancestral forms of diversified immune receptors found in modern-day vertebrates.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of VCBP3 from Branchiostoma floridae.
      Hernandez Prada, J.A.,Haire, R.N.,Cannon, J.P.,Litman, G.W.,Ostrov, D.A.
      (2004) Acta Crystallogr.,Sect.D 60: 2022


    Organizational Affiliation

    Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida 32610, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
variable region-containing chitin-binding protein 3
A
135Branchiostoma floridaeMutation(s): 0 
Gene Names: VCBP3
Find proteins for Q8I9N0 (Branchiostoma floridae)
Go to UniProtKB:  Q8I9N0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.127 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.191α = 90.00
b = 59.191β = 90.00
c = 79.263γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
SHELXL-97refinement
SOLVEphasing
SHELXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance