2WNG | pdb_00002wng

complete extracellular structure of human signal regulatory protein (SIRP) alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.271 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history

Literature

Structure of Signal-Regulatory Protein Alpha: A Link to Antigen Receptor Evolution.

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

(2009) J Biological Chem 284: 26613

  • DOI: https://doi.org/10.1074/jbc.M109.017566
  • Primary Citation Related Structures: 
    2WNG

  • PubMed Abstract: 

    Signal-regulatory protein alpha (SIRPalpha) is a myeloid membrane receptor that interacts with the membrane protein CD47, a marker of self. We have solved the structure of the complete extracellular portion of SIRPalpha, comprising three immunoglobulin superfamily domains, by x-ray crystallography to 2.5 A resolution. These data, together with previous data on the N-terminal domain and its ligand CD47 (possessing a single immunoglobulin superfamily domain), show that the CD47-SIRPalpha interaction will span a distance of around 14 nm between interacting cells, comparable with that of an immunological synapse. The N-terminal (V-set) domain mediates binding to CD47, and the two others are found to be constant (C1-set) domains. C1-set domains are restricted to proteins involved in vertebrate antigen recognition: T cell antigen receptors, immunoglobulins, major histocompatibility complex antigens, tapasin, and beta2-microglobulin. The domains of SIRPalpha (domains 2 and 3) are structurally more similar to C1-set domains than any cell surface protein not involved in antigen recognition. This strengthens the suggestion from sequence analysis that SIRP is evolutionarily closely related to antigen recognition proteins.


  • Organizational Affiliation
    • Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 36.43 kDa 
  • Atom Count: 2,413 
  • Modeled Residue Count: 307 
  • Deposited Residue Count: 327 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1327Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P78324 (Homo sapiens)
Explore P78324 
Go to UniProtKB:  P78324
PHAROS:  P78324
GTEx:  ENSG00000198053 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78324
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P78324-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
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: 2.49 Å
  • R-Value Free:  0.271 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.41α = 90
b = 84.37β = 90
c = 98.86γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-03
    Changes: Data collection, Derived calculations, Other, Source and taxonomy
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.6: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.7: 2024-11-06
    Changes: Structure summary