5O35

Structure of complement proteins complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Regulator-dependent mechanisms of C3b processing by factor I allow differentiation of immune responses.

Xue, X.Wu, J.Ricklin, D.Forneris, F.Di Crescenzio, P.Schmidt, C.Q.Granneman, J.Sharp, T.H.Lambris, J.D.Gros, P.

(2017) Nat Struct Mol Biol 24: 643-651

  • DOI: https://doi.org/10.1038/nsmb.3427
  • Primary Citation of Related Structures:  
    5O32, 5O35

  • PubMed Abstract: 

    The complement system labels microbes and host debris for clearance. Degradation of surface-bound C3b is pivotal to direct immune responses and protect host cells. How the serine protease factor I (FI), assisted by regulators, cleaves either two or three distant peptide bonds in the CUB domain of C3b remains unclear. We present a crystal structure of C3b in complex with FI and regulator factor H (FH; domains 1-4 with 19-20). FI binds C3b-FH between FH domains 2 and 3 and a reoriented C3b C-terminal domain and docks onto the first scissile bond, while stabilizing its catalytic domain for proteolytic activity. One cleavage in C3b does not affect its overall structure, whereas two cleavages unfold CUB and dislodge the thioester-containing domain (TED), affecting binding of regulators and thereby determining the number of cleavages. These data explain how FI generates late-stage opsonins iC3b or C3dg in a context-dependent manner, to react to foreign, danger or healthy self signals.


  • Organizational Affiliation

    Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C3645Homo 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C3915Homo 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Complement factor H,Complement factor H383Homo sapiensMutation(s): 0 
Gene Names: CFHHFHF1HF2
UniProt & NIH Common Fund Data Resources
Find proteins for P08603 (Homo sapiens)
Explore P08603 
Go to UniProtKB:  P08603
PHAROS:  P08603
GTEx:  ENSG00000000971 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08603
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.9α = 90
b = 142.9β = 90
c = 312.721γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesR01AI030040-16
NWONetherlandsSpinoza 01.80.104.00
European Research CouncilNetherlandsAdG 233229

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Database references
  • Version 1.3: 2018-01-31
    Changes: Author supporting evidence
  • Version 1.4: 2019-10-16
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary