2JJS

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 2.1 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: 10.1016/j.molcel.2008.05.026
  • Primary Citation of Related Structures:  
    2JJW, 2JJV, 2JJU, 2JJT, 2JJS, 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) ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1A, B126Homo sapiensMutation(s): 0 
Gene Names: SIRPA, BIT, MFR, MYD1, PTPNS1, SHPS1, SIRP
UniProt & NIH Common Fund Data Resources
Find proteins for P78324 (Homo sapiens)
Explore P78324 
Go to UniProtKB:  P78324
PHAROS:  P78324
GTEx:  ENSG00000198053
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LEUKOCYTE SURFACE ANTIGEN CD47C, D127Homo sapiensMutation(s): 1 
Gene Names: CD47, MER6
UniProt & NIH Common Fund Data Resources
Find proteins for Q08722 (Homo sapiens)
Explore Q08722 
Go to UniProtKB:  Q08722
PHAROS:  Q08722
GTEx:  ENSG00000196776
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
 E [auth A], K [auth B], Q [auth C], R [auth C], W [auth D], X [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
IOD
Query on IOD
Download Ideal Coordinates CCD File 
AA [auth D] , BA [auth D] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , L [auth B] , 
AA [auth D],  BA [auth D],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  L [auth B],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  S [auth C],  T [auth C],  U [auth C],  V [auth C],  Y [auth D],  Z [auth D]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA		C, DL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.477α = 90
b = 72.41β = 95.01
c = 89.826γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

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