6YSQ

The hC4Nb8 complement inhibitory nanobody in complex with C4b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

An Ultrahigh-Affinity Complement C4b-Specific Nanobody Inhibits In Vivo Assembly of the Classical Pathway Proconvertase.

Zarantonello, A.Presumey, J.Simoni, L.Yalcin, E.Fox, R.Hansen, A.Olesen, H.G.Thiel, S.Johnson, M.B.Stevens, B.Laursen, N.S.Carroll, M.C.Andersen, G.R.

(2020) J Immunol 205: 1678-1694

  • DOI: 10.4049/jimmunol.2000528
  • Primary Citation of Related Structures:  
    6YSQ

  • PubMed Abstract: 
  • The classical and lectin pathways of the complement system are important for the elimination of pathogens and apoptotic cells and stimulation of the adaptive immune system. Upon activation of these pathways, complement component C4 is proteolytically cleaved, and the major product C4b is deposited on the activator, enabling assembly of a C3 convertase and downstream alternative pathway amplification ...

    The classical and lectin pathways of the complement system are important for the elimination of pathogens and apoptotic cells and stimulation of the adaptive immune system. Upon activation of these pathways, complement component C4 is proteolytically cleaved, and the major product C4b is deposited on the activator, enabling assembly of a C3 convertase and downstream alternative pathway amplification. Although excessive activation of the lectin and classical pathways contributes to multiple autoimmune and inflammatory diseases and overexpression of a C4 isoform has recently been linked to schizophrenia, a C4 inhibitor and structural characterization of the convertase formed by C4b is lacking. In this study, we present the nanobody hC4Nb8 that binds with picomolar affinity to human C4b and potently inhibits in vitro complement C3 deposition through the classical and lectin pathways in human serum and in mouse serum. The crystal structure of the C4b:hC4Nb8 complex and a three-dimensional reconstruction of the C4bC2 proconvertase obtained by electron microscopy together rationalize how hC4Nb8 prevents proconvertase assembly through recognition of a neoepitope exposed in C4b and reveals a unique C2 conformation compared with the alternative pathway proconvertase. On human induced pluripotent stem cell-derived neurons, the nanobody prevents C3 deposition through the classical pathway. Furthermore, hC4Nb8 inhibits the classical pathway-mediated immune complex delivery to follicular dendritic cells in vivo. The hC4Nb8 represents a novel ultrahigh-affinity inhibitor of the classical and lectin pathways of the complement cascade under both in vitro and in vivo conditions.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, DK8000 Aarhus, Denmark; gra@mbg.au.dk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C4 beta chainA, D [auth B]656Homo sapiensMutation(s): 0 
Gene Names: C4BCO4CPAMD3C4B_2
Find proteins for P0C0L5 (Homo sapiens)
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Go to UniProtKB:  P0C0L5
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PHAROS:  P0C0L5
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C4-A alpha chainB [auth C], E [auth D]690Homo sapiensMutation(s): 2 
Gene Names: C4ACO4CPAMD2
Find proteins for P0C0L4 (Homo sapiens)
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Go to UniProtKB:  P0C0L4
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PHAROS:  P0C0L4
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C4 gamma chainC [auth E], F291Homo sapiensMutation(s): 0 
Gene Names: C4BCO4CPAMD3C4B_2
Find proteins for P0C0L5 (Homo sapiens)
Explore P0C0L5 
Go to UniProtKB:  P0C0L5
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PHAROS:  P0C0L5
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
hC4Nb8 nanobodyG, H132Escherichia coliMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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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-glucopyranoseI, J, K, L3 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.2α = 90
b = 89.51β = 97.552
c = 231.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR155-2015-2666

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-08-19
    Changes: Database references, Structure summary
  • Version 2.2: 2020-09-16
    Changes: Database references
  • Version 3.0: 2021-05-05
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary