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RCSB PDB - 2WII: Complement C3b in complex with factor H domains 1-4

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Complement C3b in complex with factor H domains 1-4




    This is version 2.2 of the entry. See complete history



    Structure of complement fragment C3b-factor H and implications for host protection by complement regulators.

    Wu, J.Wu, Y.Q.Ricklin, D.Janssen, B.J.Lambris, J.D.Gros, P.

    (2009) Nat Immunol 10: 728-733

    • PubMed19503104 Search on PubMedSearch on PubMed Central
    • DOI: https://doi.org/10.1038/ni.1755

    • PubMed Abstract: 

      Factor H (FH) is an abundant regulator of complement activation and protects host cells from self-attack by complement. Here we provide insight into the regulatory activity of FH by solving the crystal structure of the first four domains of FH in complex with its target, complement fragment C3b. FH interacted with multiple domains of C3b, covering a large, extended surface area. The structure indicated that FH destabilizes the C3 convertase by competition and electrostatic repulsion and that FH enables proteolytic degradation of C3b by providing a binding platform for protease factor I while stabilizing the overall domain arrangement of C3b. Our results offer general models for complement regulation and provide structural explanations for disease-related mutations in the genes encoding both FH and C3b.


    • Organizational Affiliation

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

    Macromolecule Content

    • Total Structure Weight: 209.59 kDa 
    • Atom Count: 14,442 
    • Modelled Residue Count: 1,781 
    • Deposited Residue Count: 1,837 
    • Unique protein chains: 3

    Find similar proteins by:

    (by identity cutoff)  |  3D Structure

    Find similar proteins by:

    (by identity cutoff)  |  3D Structure

    Find similar proteins by:

    (by identity cutoff)  |  3D Structure

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    Entity ID: 4
    MoleculeChains Length2D Diagram Glycosylation3D Interactions
    beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

    D

    6N-Glycosylation
    Glycosylation Resources

    GlyTouCan:  G52684JK

    GlyCosmos:  G52684JK

    GlyGen:  G52684JK

    Ligands 3 Unique
    IDChains Name / Formula / InChI Key2D Diagram3D Interactions
    NAG
    Query on NAG

    Download Ideal Coordinates CCD File 
    V [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
    C8 H15 N O6
    OVRNDRQMDRJTHS-FMDGEEDCSA-N
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 

    F [auth A]
    G [auth A]
    H [auth A]
    I [auth B]
    J [auth B]

    F [auth A],
    G [auth A],
    H [auth A],
    I [auth B],
    J [auth B],
    K [auth B],
    L [auth B],
    M [auth B],
    N [auth B],
    O [auth B],
    P [auth B],
    Q [auth B],
    R [auth B],
    S [auth B],
    T [auth B],
    U [auth B],
    W [auth C]

    GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
    CA
    Query on CA

    Download Ideal Coordinates CCD File 
    E [auth A]CALCIUM ION
    Ca
    BHPQYMZQTOCNFJ-UHFFFAOYSA-N

    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.70 Å
    • R-Value Free:  0.252 (Depositor), 0.240 (DCC) 
    • R-Value Work:  0.217 (Depositor), 0.200 (DCC) 
    • R-Value Observed: 0.218 (Depositor) 

    Unit Cell:

    Length ( Å )Angle ( ˚ )
    a = 223.489α = 90
    b = 84.946β = 90
    c = 128.77γ = 90

    Software Package:

    Software NamePurpose
    PHENIXrefinement
    MOSFLMdata reduction
    SCALAdata scaling
    PHASERphasing

    Revision History  (Full details and data files)

    • Version 1.0: 2009-06-09
      Type: Initial release
    • Version 1.1: 2011-05-08
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2018-02-28
      Changes: Database references, Source and taxonomy
    • Version 2.0: 2020-07-29
      Type: Remediation
      Reason: Carbohydrate remediation
      Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
    • Version 2.1: 2023-12-13
      Changes: Data collection, Database references, Refinement description, Structure summary
    • Version 2.2: 2024-10-16
      Changes: Structure summary