4CMM

Structure of human CD47 in complex with human Signal Regulatory Protein (SIRP) alpha v1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Polymorphisms in the Human Inhibitory Signal-Regulatory Protein Alpha Do not Affect Binding to its Ligand Cd47.

Hatherley, D.Lea, S.M.Johnson, S.Barclay, A.N.

(2014) J.Biol.Chem. 289: 10024

  • DOI: 10.1074/jbc.M114.550558

  • PubMed Abstract: 
  • CD47 is a widely distributed membrane protein that interacts with signal-regulatory protein α (SIRPα), an inhibitory receptor on myeloid cells that gives a "don't-eat-me" signal. Manipulation of the interaction is of considerable interest in the immu ...

    CD47 is a widely distributed membrane protein that interacts with signal-regulatory protein α (SIRPα), an inhibitory receptor on myeloid cells that gives a "don't-eat-me" signal. Manipulation of the interaction is of considerable interest in the immunotherapy of cancer and in xenotransplantation. The amino-terminal ligand binding domain of SIRPα is highly polymorphic in contrast to the single Ig-like domain of CD47. There is confusion as to whether the polymorphisms will affect ligand binding, but this is an important point for this interaction and other paired receptors being considered as targets for therapy. We show by x-ray crystallography that one human SIRPα allele differing in 13 amino acid residues has a very similar binding site and that several different alleles all bind CD47 with similar affinity as expected because the residues are mostly surface-exposed and distant from the binding site. A peptide from the binding site of CD47 has been reported to mimic the CD47 interaction with SIRPα, but we could find no binding. We discuss the possible pitfalls in determining the affinity of weak interactions and also speculate on how SIRPα polymorphisms may have been selected by pathogens and how this may also be true in other paired receptors such as the KIRs.


    Organizational Affiliation

    From the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
A
127Homo sapiensMutation(s): 0 
Gene Names: SIRPA (BIT, MFR, MYD1, PTPNS1, SHPS1, SIRP)
Find proteins for P78324 (Homo sapiens)
Go to Gene View: SIRPA
Go to UniProtKB:  P78324
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
LEUKOCYTE SURFACE ANTIGEN CD47
B
127Homo sapiensMutation(s): 1 
Gene Names: CD47 (MER6)
Find proteins for Q08722 (Homo sapiens)
Go to Gene View: CD47
Go to UniProtKB:  Q08722
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
B
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 67.390α = 90.00
b = 32.470β = 115.06
c = 69.610γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-04-16
    Type: Database references