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 

Starting Models: experimental
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This is version 1.3 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: 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. 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COMPLEMENT C3 BETA CHAIN
A, D
645Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
GTEx:  ENSG00000125730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01024-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COMPLEMENT C3B ALPHA' CHAIN
B, E
915Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
GTEx:  ENSG00000125730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COMPLEMENT RECEPTOR TYPE 1
C, F
196Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P17927 (Homo sapiens)
Explore P17927 
Go to UniProtKB:  P17927
PHAROS:  P17927
GTEx:  ENSG00000203710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17927
Sequence Annotations
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  • Reference Sequence
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

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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary