4M76

Integrin I domain of complement receptor 3 in complex with C3d


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.804 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.USA 110: 16426-16431

  • DOI: 10.1073/pnas.1311261110

  • 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 bet ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Complement C3
A
298Homo sapiensMutation(s): 1 
Gene Names: C3 (CPAMD1)
Find proteins for P01024 (Homo sapiens)
Go to Gene View: C3
Go to UniProtKB:  P01024
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Integrin alpha-M
B
198Homo sapiensMutation(s): 2 
Gene Names: ITGAM (CD11B, CR3A)
Find proteins for P11215 (Homo sapiens)
Go to Gene View: ITGAM
Go to UniProtKB:  P11215
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A, B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.804 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 144.460α = 90.00
b = 65.120β = 115.69
c = 62.540γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-23
    Type: Database references
  • Version 1.2: 2013-11-06
    Type: Structure summary
  • Version 1.3: 2014-11-12
    Type: Structure summary