4M76

Integrin I domain of complement receptor 3 in complex with C3d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural insight on the recognition of surface-bound opsonins by the integrin I domain of complement receptor 3.

Bajic, G.Yatime, L.Sim, R.B.Vorup-Jensen, T.Andersen, G.R.

(2013) Proc Natl Acad Sci U S A 110: 16426-16431

  • DOI: https://doi.org/10.1073/pnas.1311261110
  • Primary Citation of Related Structures:  
    4M76

  • PubMed Abstract: 

    Complement receptors (CRs), expressed notably on myeloid and lymphoid cells, play an essential function in the elimination of complement-opsonized pathogens and apoptotic/necrotic cells. In addition, these receptors are crucial for the cross-talk between the innate and adaptive branches of the immune system. CR3 (also known as Mac-1, integrin αMβ2, or CD11b/CD18) is expressed on all macrophages and recognizes iC3b on complement-opsonized objects, enabling their phagocytosis. We demonstrate that the C3d moiety of iC3b harbors the binding site for the CR3 αI domain, and our structure of the C3d:αI domain complex rationalizes the CR3 selectivity for iC3b. Based on extensive structural analysis, we suggest that the choice between a ligand glutamate or aspartate for coordination of a receptor metal ion-dependent adhesion site-bound metal ion is governed by the secondary structure of the ligand. Comparison of our structure to the CR2:C3d complex and the in vitro formation of a stable CR3:C3d:CR2 complex suggests a molecular mechanism for the hand-over of CR3-bound immune complexes from macrophages to CR2-presenting cells in lymph nodes.


  • Organizational Affiliation

    Departments of Molecular Biology and Genetics and Biomedicine, Aarhus University, DK-8000 Aarhus, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C3298Homo sapiensMutation(s): 1 
Gene Names: C3CPAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
GTEx:  ENSG00000125730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Integrin alpha-M198Homo sapiensMutation(s): 2 
Gene Names: CD11BCR3AITGAM
UniProt & NIH Common Fund Data Resources
Find proteins for P11215 (Homo sapiens)
Explore P11215 
Go to UniProtKB:  P11215
GTEx:  ENSG00000169896 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11215
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.46α = 90
b = 65.12β = 115.69
c = 62.54γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references
  • Version 1.2: 2013-11-06
    Changes: Structure summary
  • Version 1.3: 2014-11-12
    Changes: Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description