1BY2

STRUCTURE OF M2BP SCAVENGER RECEPTOR CYSTEINE-RICH DOMAIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a scavenger receptor cysteine-rich domain sheds light on an ancient superfamily.

Hohenester, E.Sasaki, T.Timpl, R.

(1999) Nat.Struct.Mol.Biol. 6: 228-232

  • DOI: 10.1038/6669

  • PubMed Abstract: 
  • Scavenger receptor cysteine-rich (SRCR) domains are found widely in cell surface molecules and in some secreted proteins, where they are thought to mediate ligand binding. We have determined the crystal structure at 2.0 A resolution of the SRCR domai ...

    Scavenger receptor cysteine-rich (SRCR) domains are found widely in cell surface molecules and in some secreted proteins, where they are thought to mediate ligand binding. We have determined the crystal structure at 2.0 A resolution of the SRCR domain of Mac-2 binding protein (M2BP), a tumor-associated antigen and matrix protein. The structure reveals a curved six-stranded beta-sheet cradling an alpha-helix. Structure-based sequence alignment demonstrates that the M2BP SRCR domain is a valid template for the entire SRCR protein superfamily. This allows an interpretation of previous mutagenesis data on ligand binding to the lymphocyte receptor CD6.


    Related Citations: 
    • The Srcr Superfamily: A Family Reminiscent of the Ig Superfamily
      Resnick, D.,Pearson, A.,Krieger, M.
      (1994) Trends Biochem.Sci. 19: 5
    • Mac-2 Binding Protein is a Cell-Adhesive Protein of the Extracellular Matrix which Self-Assembles Into Ring-Like Structures and Binds Beta1 Integrins, Collagens and Fibronectin
      Sasaki, T.,Brakebusch, C.,Engel, J.,Timpl, R.
      (1998) Embo J. 17: 1606


    Organizational Affiliation

    Department of Crystallography, Birkbeck College, University of London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAC-2 BINDING PROTEIN
A
119Homo sapiensMutation(s): 0 
Gene Names: LGALS3BP (M2BP)
Find proteins for Q08380 (Homo sapiens)
Go to Gene View: LGALS3BP
Go to UniProtKB:  Q08380
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.186 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 44.630α = 90.00
b = 44.630β = 90.00
c = 134.540γ = 90.00
Software Package:
Software NamePurpose
CCP4phasing
CCP4data scaling
MOSFLMdata reduction
CCP4model building
X-PLORrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance