Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12926.30 
• Atom Count: 846 
• Residue Count: 119 
• Unique protein chains: 1

1BY2

STRUCTURE OF M2BP SCAVENGER RECEPTOR CYSTEINE-RICH DOMAIN

• DOI: 10.2210/pdb1BY2/pdb

• Classification: EXTRACELLULAR MODULE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens


• Deposited: 1998-10-23 Released: 1999-05-18 
• Deposition Author(s): Hohenester, E., Sasaki, T., Timpl, R.

---

Experimental Data Snapshot

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

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

• PubMed: 10074941 
• 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 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
Molecule	Chains	Sequence Length	Organism	Details
MAC-2 BINDING PROTEIN	A	119	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 44.630	α = 90.00
b = 44.630	β = 90.00
c = 134.540	γ = 90.00

Software Package:

Software Name	Purpose
CCP4	phasing
CCP4	data scaling
MOSFLM	data reduction
CCP4	model building
X-PLOR	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-10-23 
• Released Date: 1999-05-18 
• Deposition Author(s): Hohenester, E., Sasaki, T., Timpl, R.

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