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 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 3.2 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: https://doi.org/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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C4 beta chainA,
D [auth B]
656Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L5 (Homo sapiens)
Explore P0C0L5 
Go to UniProtKB:  P0C0L5
PHAROS:  P0C0L5
GTEx:  ENSG00000224389 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0L5
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0C0L5-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C4-A alpha chainB [auth C],
E [auth D]
690Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L4 (Homo sapiens)
Explore P0C0L4 
Go to UniProtKB:  P0C0L4
PHAROS:  P0C0L4
GTEx:  ENSG00000244731 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0L4
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0C0L4-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C4 gamma chainC [auth E],
F
291Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0L5 (Homo sapiens)
Explore P0C0L5 
Go to UniProtKB:  P0C0L5
PHAROS:  P0C0L5
GTEx:  ENSG00000224389 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0L5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
hC4Nb8 nanobody
G, H
132Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains 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
I, J, K, L
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
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

View Full Validation Report



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
  • Version 3.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 3.2: 2024-10-09
    Changes: Structure summary