5FOA

Crystal Structure of Human Complement C3b in complex with DAF (CCP2-4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.19 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 

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

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

Find similar proteins by: Sequence  |  Structure

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

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DECAY ACCELERATING FACTOR, CD55
E, F
194Homo sapiensMutation(s): 0 
Gene Names: CD55CRDAF
Find proteins for P08174 (Homo sapiens)
Go to UniProtKB:  P08174
NIH Common Fund Data Resources
PHAROS  P08174
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.19 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.271 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.429α = 90
b = 142.378β = 90
c = 323.697γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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