7TE3

Crystal Structure of a Double Loop Deletion Mutant in gC1qR/C1qBP/HABP-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

gC1qR/C1qBP/HABP-1: Structural Analysis of the Trimeric Core Region, Interactions With a Novel Panel of Monoclonal Antibodies, and Their Influence on Binding to FXII.

Zhang, Y.Vontz, A.J.Kallenberger, E.M.Xu, X.Ploscariu, N.T.Ramyar, K.X.Garcia, B.L.Ghebrehiwet, B.Geisbrecht, B.V.

(2022) Front Immunol 13: 887742-887742

  • DOI: https://doi.org/10.3389/fimmu.2022.887742
  • Primary Citation of Related Structures:  
    7TE3

  • PubMed Abstract: 

    The protein gC1qR/C1qBP/HABP-1 plays an essential role in mitochondrial biogenesis, but becomes localized at the cellular surface in numerous pathophysiological states. When this occurs on endothelial cells, surface-exposed gC1qR activates the classical pathway of complement. It also promotes assembly of a multi-protein complex comprised of coagulation factor XII (FXII), pre-kallikrein (PK), and high-molecular weight kininogen (HMWK) that activates the contact system and the kinin-generating system. Since surface-exposed gC1qR triggers intravascular inflammatory pathways, there is interest in identifying molecules that block gC1qR function. Here we further that objective by reporting the outcome of a structure/function investigation of gC1qR, its interactions with FXII, and the impact of a panel of monoclonal anti-gC1qR antibodies on FXII binding to gC1qR. Although deletion mutants have been used extensively to assess gC1qR function, none of these proteins have been characterized structurally. To that end, we determined a 2.2 Å resolution crystal structure of a gC1qR mutant lacking both of its acidic loops, but which retained nanomolar-affinity binding to FXII and FXIIa. This structure revealed that the trimeric gC1qR assembly was maintained despite loss of roughly thirty residues. Characterization of a novel panel of anti-gC1qR monoclonal antibodies identified several with biochemical properties distinct from previously described antibodies, as well as one which bound to the first acidic loop of gC1qR. Intriguingly, we found that each of these antibodies could partly inhibit binding of FXII and FXIIa to gC1qR. Based on these results and previously published studies, we offer new perspectives for developing gC1qR inhibitors.


  • Organizational Affiliation

    Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, KS, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement component 1 Q subcomponent-binding protein, mitochondrial177Homo sapiensMutation(s): 0 
Gene Names: C1QBPGC1QBPHABP1SF2P32
UniProt & NIH Common Fund Data Resources
Find proteins for Q07021 (Homo sapiens)
Explore Q07021 
Go to UniProtKB:  Q07021
PHAROS:  Q07021
GTEx:  ENSG00000108561 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07021
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.238 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.529α = 90
b = 80.529β = 90
c = 114.552γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM140852

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description