1BY2

STRUCTURE OF M2BP SCAVENGER RECEPTOR CYSTEINE-RICH DOMAIN

• PDB DOI: https://doi.org/10.2210/pdb1BY2/pdb

• Classification: EXTRACELLULAR MODULE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.186 
• R-Value Observed: 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 Biol 6: 228-232

• PubMed: 10074941 
• DOI: https://doi.org/10.1038/6669
• Primary Citation of Related Structures:  
  1BY2


• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.93 kDa 
• Atom Count: 903 
• Modelled Residue Count: 112 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAC-2 BINDING PROTEIN	A	119	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q08380 (Homo sapiens) Explore Q08380  Go to UniProtKB:  Q08380
PHAROS:  Q08380 GTEx:  ENSG00000108679
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q08380-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.218 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.63	α = 90
b = 44.63	β = 90
c = 134.54	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-11-20
  Changes: Advisory, Data collection, Database references, Structure summary