Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 11.32 kDa 
• Atom Count: 847 
• Modelled Residue Count: 101 
• Deposited Residue Count: 101 
• Unique protein chains: 1

2JA4

Crystal structure of CD5 domain III reveals the fold of a group B scavenger cysteine-rich receptor

• PDB DOI: 10.2210/pdb2JA4/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2006-11-21 Released: 2007-03-06 
• Deposition Author(s): Rodamilans, B., Munoz, I.G., Sarrias, M.R., Lozano, F., Blanco, F.J., Montoya, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.248 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Crystal Structure of the Third Extracellular Domain of Cd5 Reveals the Fold of a Group B Scavenger Cysteine-Rich Receptor Domain.

Rodamilans, B., Munoz, I.G., Bragado-Nilsson, E., Sarrias, M.R., Padilla, O., Blanco, F.J., Lozano, F., Montoya, G.

(2007) J Biol Chem 282: 12669

• PubMed: 17322294 
• DOI: 10.1074/jbc.M611699200
• Primary Citation of Related Structures:  
  2JA4, 2OTT


• PubMed Abstract: 
  

Scavenger receptor cysteine-rich (SRCR) domains are ancient protein modules widely found among cell surface and secreted proteins of the innate and adaptive immune system, where they mediate ligand binding. We have solved the crystal structure at 2.2 A of resolution of the SRCR CD5 domain III, a human lymphocyte receptor involved in the modulation of antigen specific receptor-mediated T cell activation and differentiation signals. The first structure of a member of a group B SRCR domain reveals the fold of this ancient protein module into a central core formed by two antiparallel beta-sheets and one alpha-helix, illustrating the conserved core at the protein level of genes coding for group A and B members of the SRCR superfamily. The novel SRCR group B structure permits the interpretation of site-directed mutagenesis data on the binding of activated leukocyte cell adhesion molecule (ALCAM/CD166) binding to CD6, a closely related lymphocyte receptor homologue to CD5.

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Organizational Affiliation: 

Spanish National Cancer Center (CNIO), Structural Biology and Biocomputing Program, c/Melchor Fernandez Almagro 3, 28029 Madrid, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-CELL SURFACE GLYCOPROTEIN CD5	A	101	Homo sapiens	Mutation(s): 0  Gene Names: CD5, LEU1
UniProt & NIH Common Fund Data Resources
Find proteins for P06127 (Homo sapiens) Explore P06127  Go to UniProtKB:  P06127
PHAROS:  P06127

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.248 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.931	α = 90
b = 62.931	β = 90
c = 72.564	γ = 120

Software Package:

Software Name	Purpose
ARP/wARP	model building
SCALEPACK	data scaling
BNP	phasing
SHARP	phasing
SOLOMON	phasing
ARP/wARP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-21 
• Released Date: 2007-03-06 
Deposition Author(s): Rodamilans, B., Munoz, I.G., Sarrias, M.R., Lozano, F., Blanco, F.J., Montoya, G.

Revision History  

• Version 1.0: 2007-03-06
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-06-28
  Changes: Refinement description