5FO8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report



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:  
    5FO7, 5FO9, 5FO8, 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 stru ...

    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 A645Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
EC: 3.4.21.47
Find proteins for P01024 (Homo sapiens)
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Go to UniProtKB:  P01024
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PHAROS:  P01024
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COMPLEMENT C3 B915Homo sapiensMutation(s): 0 
Gene Names: C3CPAMD1
EC: 3.4.21.47
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
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PHAROS:  P01024
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MEMBRANE COFACTOR PROTEIN C252Homo sapiensMutation(s): 0 
Gene Names: CD46MCPMIC10
Find proteins for P15529 (Homo sapiens)
Explore P15529 
Go to UniProtKB:  P15529
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PHAROS:  P15529
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.83α = 90
b = 130.63β = 90
c = 233.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata 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
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary