6KMV | pdb_00006kmv

caspase-11 C254A P22/P10 in complex with mouse GSDMD-C domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 
    0.252 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Mechanism for GSDMD Targeting by Autoprocessed Caspases in Pyroptosis.

Wang, K.Sun, Q.Zhong, X.Zeng, M.Zeng, H.Shi, X.Li, Z.Wang, Y.Zhao, Q.Shao, F.Ding, J.

(2020) Cell 180: 941

  • DOI: https://doi.org/10.1016/j.cell.2020.02.002
  • Primary Citation of Related Structures:  
    6KMT, 6KMU, 6KMV, 6KMZ, 6KN0, 6KN1

  • PubMed Abstract: 

    The pyroptosis execution protein GSDMD is cleaved by inflammasome-activated caspase-1 and LPS-activated caspase-11/4/5. The cleavage unmasks the pore-forming domain from GSDMD-C-terminal domain. How the caspases recognize GSDMD and its connection with caspase activation are unknown. Here, we show site-specific caspase-4/11 autoprocessing, generating a p10 product, is required and sufficient for cleaving GSDMD and inducing pyroptosis. The p10-form autoprocessed caspase-4/11 binds the GSDMD-C domain with a high affinity. Structural comparison of autoprocessed and unprocessed capase-11 identifies a β sheet induced by the autoprocessing. In caspase-4/11-GSDMD-C complex crystal structures, the β sheet organizes a hydrophobic GSDMD-binding interface that is only possible for p10-form caspase-4/11. The binding promotes dimerization-mediated caspase activation, rendering a cleavage independently of the cleavage-site tetrapeptide sequence. Crystal structure of caspase-1-GSDMD-C complex shows a similar GSDMD-recognition mode. Our study reveals an unprecedented substrate-targeting mechanism for caspases. The hydrophobic interface suggests an additional space for developing inhibitors specific for pyroptotic caspases.


  • Organizational Affiliation
    • Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, National Institute of Biological Sciences, 102206 Beijing, China; National Institute of Biological Sciences, Beijing, 102206 Beijing, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-4161Mus musculusMutation(s): 1 
Gene Names: Casp4Casp11CasplIch3
EC: 3.4.22.64
UniProt & NIH Common Fund Data Resources
Find proteins for P70343 (Mus musculus)
Explore P70343 
Go to UniProtKB:  P70343
IMPC:  MGI:107700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70343
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-4
B, V
167Mus musculusMutation(s): 1 
Gene Names: Casp4Casp11CasplIch3
EC: 3.4.22.64
UniProt & NIH Common Fund Data Resources
Find proteins for P70343 (Mus musculus)
Explore P70343 
Go to UniProtKB:  P70343
IMPC:  MGI:107700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70343
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gasdermin-D
C, G, O
198Mus musculusMutation(s): 0 
Gene Names: Gsdmdc1Gsdmd
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D8T2 (Mus musculus)
Explore Q9D8T2 
Go to UniProtKB:  Q9D8T2
IMPC:  MGI:1916396
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D8T2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Gasdermin-D197Mus musculusMutation(s): 0 
Gene Names: Gsdmdc1Gsdmd
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D8T2 (Mus musculus)
Explore Q9D8T2 
Go to UniProtKB:  Q9D8T2
IMPC:  MGI:1916396
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D8T2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-4DA [auth d],
E,
F,
Z
166Mus musculusMutation(s): 1 
Gene Names: Casp4Casp11CasplIch3
EC: 3.4.22.64
UniProt & NIH Common Fund Data Resources
Find proteins for P70343 (Mus musculus)
Explore P70343 
Go to UniProtKB:  P70343
IMPC:  MGI:107700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70343
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Gasdermin-D191Mus musculusMutation(s): 0 
Gene Names: Gsdmdc1Gsdmd
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D8T2 (Mus musculus)
Explore Q9D8T2 
Go to UniProtKB:  Q9D8T2
IMPC:  MGI:1916396
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D8T2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-4
I, M, N, Q, Y
165Mus musculusMutation(s): 1 
Gene Names: Casp4Casp11CasplIch3
EC: 3.4.22.64
UniProt & NIH Common Fund Data Resources
Find proteins for P70343 (Mus musculus)
Explore P70343 
Go to UniProtKB:  P70343
IMPC:  MGI:107700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70343
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-4149Mus musculusMutation(s): 1 
Gene Names: Casp4Casp11CasplIch3
EC: 3.4.22.64
UniProt & NIH Common Fund Data Resources
Find proteins for P70343 (Mus musculus)
Explore P70343 
Go to UniProtKB:  P70343
IMPC:  MGI:107700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70343
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Gasdermin-DEA [auth e],
L,
P
214Mus musculusMutation(s): 0 
Gene Names: Gsdmdc1Gsdmd
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D8T2 (Mus musculus)
Explore Q9D8T2 
Go to UniProtKB:  Q9D8T2
IMPC:  MGI:1916396
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D8T2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-4CA [auth c],
R
150Mus musculusMutation(s): 1 
Gene Names: Casp4Casp11CasplIch3
EC: 3.4.22.64
UniProt & NIH Common Fund Data Resources
Find proteins for P70343 (Mus musculus)
Explore P70343 
Go to UniProtKB:  P70343
IMPC:  MGI:107700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70343
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-4165Mus musculusMutation(s): 1 
Gene Names: Casp4Casp11CasplIch3
EC: 3.4.22.64
UniProt & NIH Common Fund Data Resources
Find proteins for P70343 (Mus musculus)
Explore P70343 
Go to UniProtKB:  P70343
IMPC:  MGI:107700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70343
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Gasdermin-D199Mus musculusMutation(s): 0 
Gene Names: Gsdmdc1Gsdmd
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D8T2 (Mus musculus)
Explore Q9D8T2 
Go to UniProtKB:  Q9D8T2
IMPC:  MGI:1916396
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D8T2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Gasdermin-DAA [auth a]196Mus musculusMutation(s): 0 
Gene Names: Gsdmdc1Gsdmd
UniProt & NIH Common Fund Data Resources
Find proteins for Q9D8T2 (Mus musculus)
Explore Q9D8T2 
Go to UniProtKB:  Q9D8T2
IMPC:  MGI:1916396
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9D8T2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-488Mus musculusMutation(s): 0 
Gene Names: Casp4Casp11CasplIch3
EC: 3.4.22.64
UniProt & NIH Common Fund Data Resources
Find proteins for P70343 (Mus musculus)
Explore P70343 
Go to UniProtKB:  P70343
IMPC:  MGI:107700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70343
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-4SA [auth s]87Mus musculusMutation(s): 0 
Gene Names: Casp4Casp11CasplIch3
EC: 3.4.22.64
UniProt & NIH Common Fund Data Resources
Find proteins for P70343 (Mus musculus)
Explore P70343 
Go to UniProtKB:  P70343
IMPC:  MGI:107700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70343
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free:  0.252 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.798α = 92.43
b = 139.207β = 99.06
c = 175.942γ = 96.35
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2025-03-12
    Changes: Database references, Structure summary