6Z6V

Globular head of C1q in complex with the nanobody C1qNb75


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Functional and Structural Characterization of a Potent C1q Inhibitor Targeting the Classical Pathway of the Complement System.

Laursen, N.S.Pedersen, D.V.Gytz, H.Zarantonello, A.Bernth Jensen, J.M.Hansen, A.G.Thiel, S.Andersen, G.R.

(2020) Front Immunol 11: 1504-1504

  • DOI: https://doi.org/10.3389/fimmu.2020.01504
  • Primary Citation of Related Structures:  
    6Z6V

  • PubMed Abstract: 

    The classical pathway of complement is important for protection against pathogens and in maintaining tissue homeostasis, but excessive or aberrant activation is directly linked to numerous pathologies. We describe the development and in vitro characterization of C1qNb75, a single domain antibody (nanobody) specific for C1q, the pattern recognition molecule of the classical pathway. C1qNb75 binds to the globular head modules of human C1q with sub-nanomolar affinity and impedes classical pathway mediated hemolysis by IgG and IgM. Crystal structure analysis revealed that C1qNb75 recognizes an epitope primarily located in the C1q B-chain that overlaps with the binding sites of IgG and IgM. Thus, C1qNb75 competitively prevents C1q from binding to IgG and IgM causing blockade of complement activation by the classical pathway. Overall, C1qNb75 represents a high-affinity nanobody-based inhibitor of IgG- and IgM-mediated activation of the classical pathway and may serve as a valuable reagent in mechanistic and functional studies of complement, and as an efficient inhibitor of complement under conditions of excessive CP activation.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Center for Structural Biology, Aarhus University, Aarhus, Denmark.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C1q subcomponent subunit A
A, D
136Homo sapiensMutation(s): 0 
Gene Names: C1QA
UniProt & NIH Common Fund Data Resources
Find proteins for P02745 (Homo sapiens)
Explore P02745 
Go to UniProtKB:  P02745
PHAROS:  P02745
GTEx:  ENSG00000173372 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02745
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P02745-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C1q subcomponent subunit B
B, E
141Homo sapiensMutation(s): 0 
Gene Names: C1QB
UniProt & NIH Common Fund Data Resources
Find proteins for P02746 (Homo sapiens)
Explore P02746 
Go to UniProtKB:  P02746
PHAROS:  P02746
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02746
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C1q subcomponent subunit C
C, F
139Homo sapiensMutation(s): 0 
Gene Names: C1QCC1QG
UniProt & NIH Common Fund Data Resources
Find proteins for P02747 (Homo sapiens)
Explore P02747 
Go to UniProtKB:  P02747
PHAROS:  P02747
GTEx:  ENSG00000159189 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02747
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody C1q75
G, H
131Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.816α = 90
b = 119.744β = 90
c = 131.772γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR155-2015-2666

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2020-09-16
    Changes: Database references, Structure summary
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description