2JJT

Structure of human CD47 in complex with human signal regulatory protein (SIRP) alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 

Starting Model: experimental
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This is version 2.3 of the entry. See complete history


Literature

Paired receptor specificity explained by structures of signal regulatory proteins alone and complexed with CD47.

Hatherley, D.Graham, S.C.Turner, J.Harlos, K.Stuart, D.I.Barclay, A.N.

(2008) Mol Cell 31: 266-277

  • DOI: https://doi.org/10.1016/j.molcel.2008.05.026
  • Primary Citation of Related Structures:  
    2JJS, 2JJT, 2JJU, 2JJV, 2JJW, 2VSC

  • PubMed Abstract: 

    CD47 is a widely distributed cell-surface protein that acts a marker of self through interactions of myeloid and neural cells. We describe the high-resolution X-ray crystallographic structures of the immunoglobulin superfamily domain of CD47 alone and in complex with the N-terminal ligand-binding domain of signal regulatory protein alpha (SIRPalpha). The unusual and convoluted interacting face of CD47, comprising the N terminus and loops at the end of the domain, intercalates with the corresponding regions in SIRPalpha. We have also determined structures of the N-terminal domains of SIRPbeta, SIRPbeta(2), and SIRPgamma; proteins that are closely related to SIRPalpha but bind CD47 with negligible or reduced affinity. These results explain the specificity of CD47 for the SIRP family of paired receptors in atomic detail. Analysis of SIRPalpha polymorphisms suggests that these, as well as the activating SIRPs, may have evolved to counteract pathogen binding to the inhibitory SIRPalpha receptor.


  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
A, B
126Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P78324 (Homo sapiens)
Go to UniProtKB:  P78324
PHAROS:  P78324
GTEx:  ENSG00000198053 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LEUKOCYTE SURFACE ANTIGEN CD47
C, D
127Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q08722 (Homo sapiens)
Explore Q08722 
Go to UniProtKB:  Q08722
PHAROS:  Q08722
GTEx:  ENSG00000196776 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08722
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q08722-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.238 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.62α = 90
b = 63.72β = 90
c = 123.02γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-03-13
    Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other, Structure summary
  • Version 1.4: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 2.0: 2020-03-11
    Changes: Data collection, Other, Polymer sequence
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 2.2: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.3: 2024-10-16
    Changes: Structure summary