9EKD | pdb_00009ekd

Structure of a C1r Zymogen Fragment Bound to SALO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 
    0.286 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Blocking activation of the C1r zymogen defines a novel mode of complement inhibition.

Duan, H.Wu, W.Li, P.Bouyain, S.Garcia, B.L.Geisbrecht, B.V.

(2025) J Biological Chem 301: 108301-108301

  • DOI: https://doi.org/10.1016/j.jbc.2025.108301
  • Primary Citation of Related Structures:  
    9EKD, 9EKE

  • PubMed Abstract: 

    Many hematophagous organisms secrete inhibitors of the coagulation and complement systems as constituents of their salivary fluid. Whereas previous studies on salivary gland extracts from the sandfly Lutzomyia longipalpis identified SALO (salivary anticomplement from L. longipalpis) as a potent inhibitor of the classical complement pathway (CP), its precise mechanism of action has remained elusive. Here, we show that SALO inhibits the CP by binding selectively to the C1r zymogen. Using surface plasmon resonance, we found that SALO expressed by human embryonic kidney 293(T) cells (eSALO-WT) bound with nanomolar affinity to the zymogen of complement protease C1r (pro-C1r), but that it did not bind the enzymatically active form of C1r. To gain insight into the structural basis for CP inhibition by SALO, we solved a 3.3 Å resolution crystal structure of eSALO-WT bound to a recombinant form of C1r that was engineered to remain in a zymogen-like state (zC1r-12SP). eSALO-WT formed extensive interactions with the zymogen activation loop of zC1r-12SP, including groups derived from residues R463 and I464, which compose its scissile peptide bond. Although the interactions with R463 and I464 were mediated by side-chain sulfation of eSALO-WT at position Y51, we found that this modification enhanced the potency of SALO but was not required for its activity. Consistent with our structural observations, subsequent studies showed that eSALO-WT binding to pro-C1r blocked its activation and thereby inhibited the CP in hemolytic assays of complement function. Together, our results define a new mode of inhibiting complement by blocking the farthest upstream enzymatic reaction of the CP.


  • Organizational Affiliation
    • Department of Biochemistry & Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Salivary anti-complement proteinA,
C [auth B]
104Lutzomyia longipalpisMutation(s): 0 
UniProt
Find proteins for Q5WPZ4 (Lutzomyia longipalpis)
Explore Q5WPZ4 
Go to UniProtKB:  Q5WPZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5WPZ4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C1r subcomponentB [auth C],
D
409Homo sapiensMutation(s): 1 
Gene Names: C1R
EC: 3.4.21.41
UniProt & NIH Common Fund Data Resources
Find proteins for P00736 (Homo sapiens)
Explore P00736 
Go to UniProtKB:  P00736
PHAROS:  P00736
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00736
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
A,
C [auth B]
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free:  0.286 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.242 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.831α = 90
b = 117.831β = 90
c = 190.582γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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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: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Database references