8W18 | pdb_00008w18

The crystal structure of the Michaelis-Menten complex of a C1s/C1-INH at 3.94 Angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free: 
    0.281 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.262 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 
    0.264 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8W18

This is version 1.3 of the entry. See complete history

Literature

The Crystal Structure of the Michaelis-Menten Complex of C1 Esterase Inhibitor and C1s Reveals Novel Insights into Complement Regulation.

Garrigues, R.J.Garrison, M.P.Garcia, B.L.

(2024) J Immunol 213: 718-729

  • DOI: https://doi.org/10.4049/jimmunol.2400194
  • Primary Citation Related Structures: 
    8W18

  • PubMed Abstract: 

    The ancient arm of innate immunity known as the complement system is a blood proteolytic cascade involving dozens of membrane-bound and solution-phase components. Although many of these components serve as regulatory molecules to facilitate controlled activation of the cascade, C1 esterase inhibitor (C1-INH) is the sole canonical complement regulator belonging to a superfamily of covalent inhibitors known as serine protease inhibitors (SERPINs). In addition to its namesake role in complement regulation, C1-INH also regulates proteases of the coagulation, fibrinolysis, and contact pathways. Despite this, the structural basis for C1-INH recognition of its target proteases has remained elusive. In this study, we present the crystal structure of the Michaelis-Menten (M-M) complex of the catalytic domain of complement component C1s and the SERPIN domain of C1-INH at a limiting resolution of 3.94 Å. Analysis of the structure revealed that nearly half of the protein/protein interface is formed by residues outside of the C1-INH reactive center loop. The contribution of these residues to the affinity of the M-M complex was validated by site-directed mutagenesis using surface plasmon resonance. Parallel analysis confirmed that C1-INH-interfacing residues on C1s surface loops distal from the active site also drive affinity of the M-M complex. Detailed structural comparisons revealed differences in substrate recognition by C1s compared with C1-INH recognition and highlight the importance of exosite interactions across broader SERPIN/protease systems. Collectively, this study improves our understanding of how C1-INH regulates the classical pathway of complement, and it sheds new light on how SERPINs recognize their cognate protease targets.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC.

Macromolecule Content 

  • Total Structure Weight: 88.25 kDa 
  • Atom Count: 6,029 
  • Modeled Residue Count: 773 
  • Deposited Residue Count: 797 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Plasma protease C1 inhibitorA [auth I]395Homo sapiensMutation(s): 0 
Gene Names: SERPING1C1INC1NH
UniProt & NIH Common Fund Data Resources
Find proteins for P05155 (Homo sapiens)
Explore P05155 
Go to UniProtKB:  P05155
PHAROS:  P05155
GTEx:  ENSG00000149131 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05155
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Complement C1s subcomponent light chain251Homo sapiensMutation(s): 1 
Gene Names: C1S
EC: 3.4.21.42
UniProt & NIH Common Fund Data Resources
Find proteins for P09871 (Homo sapiens)
Explore P09871 
Go to UniProtKB:  P09871
PHAROS:  P09871
GTEx:  ENSG00000182326 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09871
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Complement C1s subcomponent heavy chainC [auth A]151Homo sapiensMutation(s): 0 
Gene Names: C1S
EC: 3.4.21.42
UniProt & NIH Common Fund Data Resources
Find proteins for P09871 (Homo sapiens)
Explore P09871 
Go to UniProtKB:  P09871
PHAROS:  P09871
GTEx:  ENSG00000182326 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09871
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.94 Å
  • R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.262 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 0.264 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.628α = 90
b = 168.628β = 90
c = 88.342γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2024-09-11
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Structure summary