5FO9

Crystal Structure of Human Complement C3b in Complex with CR1 (CCP15- 17)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 

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
  • Structures With Same Primary Citation

  • 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 p.gros@uu.nl.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C3 BETA CHAIN
A, D
645Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
Find proteins for P01024 (Homo sapiens)
Go to UniProtKB:  P01024
NIH Common Fund Data Resources
PHAROS  P01024

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT C3B ALPHA' CHAIN
B, E
915Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
Find proteins for P01024 (Homo sapiens)
Go to UniProtKB:  P01024
NIH Common Fund Data Resources
PHAROS  P01024

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
COMPLEMENT RECEPTOR TYPE 1
C, F
196Homo sapiensMutation(s): 0 
Gene Names: CR1C3BR
Find proteins for P17927 (Homo sapiens)
Go to UniProtKB:  P17927
NIH Common Fund Data Resources
PHAROS  P17927
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.253 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.32α = 82.74
b = 113.71β = 71.77
c = 138.52γ = 80.95
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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