5FO8

Crystal Structure of Human Complement C3b in Complex with MCP (CCP1-4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Regulators of Complement Activity Mediate Inhibitory Mechanisms Through a Common C3B-Binding Mode.

Forneris, F.Wu, J.Xue, X.Ricklin, D.Lin, Z.Sfyroera, G.Tzekou, A.Volokhina, E.Granneman, J.C.Hauhart, R.Bertram, P.Liszewski, M.K.Atkinson, J.P.Lambris, J.D.Gros, P.

(2016) Embo J. 35: 1133

  • DOI: 10.15252/embj.201593673
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Regulators of complement activation (RCA) inhibit complement-induced immune responses on healthy host tissues. We present crystal structures of human RCA (MCP, DAF, and CR1) and a smallpox virus homolog (SPICE) bound to complement component C3b. Our ...

    Regulators of complement activation (RCA) inhibit complement-induced immune responses on healthy host tissues. We present crystal structures of human RCA (MCP, DAF, and CR1) and a smallpox virus homolog (SPICE) bound to complement component C3b. Our structural data reveal that up to four consecutive homologous CCP domains (i-iv), responsible for inhibition, bind in the same orientation and extended arrangement at a shared binding platform on C3b. Large sequence variations in CCP domains explain the diverse C3b-binding patterns, with limited or no contribution of some individual domains, while all regulators show extensive contacts with C3b for the domains at the third site. A variation of ~100° rotation around the longitudinal axis is observed for domains binding at the fourth site on C3b, without affecting the overall binding mode. The data suggest a common evolutionary origin for both inhibitory mechanisms, called decay acceleration and cofactor activity, with variable C3b binding through domains at sites ii, iii, and iv, and provide a framework for understanding RCA disease-related mutations and immune evasion.


    Organizational Affiliation

    Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science Utrecht University, Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C3
A
645Homo sapiensMutation(s): 0 
Gene Names: C3 (CPAMD1)
Find proteins for P01024 (Homo sapiens)
Go to Gene View: C3
Go to UniProtKB:  P01024
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C3
B
915Homo sapiensMutation(s): 0 
Gene Names: C3 (CPAMD1)
Find proteins for P01024 (Homo sapiens)
Go to Gene View: C3
Go to UniProtKB:  P01024
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MEMBRANE COFACTOR PROTEIN
C
252Homo sapiensMutation(s): 0 
Gene Names: CD46 (MCP, MIC10)
Find proteins for P15529 (Homo sapiens)
Go to Gene View: CD46
Go to UniProtKB:  P15529
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.188 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.830α = 90.00
b = 130.630β = 90.00
c = 233.830γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references