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 

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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: https://doi.org/10.15252/embj.201593673
  • Primary Citation of Related Structures:  
    5FO7, 5FO8, 5FO9, 5FOA, 5FOB

  • 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 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 ...

    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 LengthOrganismDetailsImage
COMPLEMENT C3 BETA CHAIN
A, C
645Homo sapiensMutation(s): 0 
Gene Names: C3, CPAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
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UniProt GroupP01024
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COMPLEMENT C3B ALPHA CHAIN
B, D
915Homo sapiensMutation(s): 0 
Gene Names: C3, CPAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
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UniProt GroupP01024
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DECAY ACCELERATING FACTOR, CD55
E, F
194Homo sapiensMutation(s): 0 
Gene Names: CD55, CR, DAF
UniProt & NIH Common Fund Data Resources
Find proteins for P08174 (Homo sapiens)
Explore P08174 
Go to UniProtKB:  P08174
PHAROS:  P08174
Entity Groups  
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UniProt GroupP08174
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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  (Full details and data files)

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