7WR0 | pdb_00007wr0

P32 of caspase-4 C258A mutant

• PDB DOI: https://doi.org/10.2210/pdb7WR0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-01-26 Released: 2023-01-25 
• Deposition Author(s): Hou, Y.J., Zeng, H., Shao, F., Ding, J.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Structural mechanisms of calmodulin activation of Shigella effector OspC3 to ADP-riboxanate caspase-4/11 and block pyroptosis.

Hou, Y., Zeng, H., Li, Z., Feng, N., Meng, F., Xu, Y., Li, L., Shao, F., Ding, J.

(2023) Nat Struct Mol Biol 30: 261-272

• PubMed: 36624349 
• DOI: https://doi.org/10.1038/s41594-022-00888-3
• Primary Citation Related Structures: 
  7WR0, 7WR1, 7WR2, 7WR3, 7WR4, 7WR5, 7WR6


• PubMed Abstract: 
  

  The caspase-4/11-GSDMD pyroptosis axis recognizes cytosolic lipopolysaccharide for antibacterial defenses. Shigella flexneri employs an OspC3 effector to block pyroptosis by catalyzing NAD ⁺ -dependent arginine ADP-riboxanation of caspase-4/11. Here, we identify Ca ²⁺ -free calmodulin (CaM) that binds and stimulates OspC3 ADP-riboxanase activity. Crystal structures of OspC3-CaM and OspC3-caspase-4 binary complexes reveal unique CaM binding to an OspC3 N-terminal domain featuring an ADP-ribosyltransferase-like fold and specific recognition of caspase-4 by an OspC3 ankryin repeat domain, respectively. CaM-OspC3-caspase-4 ternary complex structures show that NAD ⁺ binding reorganizes the catalytic pocket, in which D231 and D177 activate the substrate arginine for initial ADP-ribosylation and ribosyl 2'-OH in the ADP-ribosylated arginine, respectively, for subsequent deamination. We also determine structures of unmodified and OspC3-ADP-riboxanated caspase-4. Mechanisms derived from this series of structures covering the entire process of OspC3 action are supported by biochemical analyses in vitro and functional validation in S. flexneri-infected mice.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
National Institute of Biological Sciences, Beijing, Beijing, China.
Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, China.
Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
National Institute of Biological Sciences, Beijing, Beijing, China. [e-mail].
Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, China. [e-mail].
Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China. [e-mail].
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
National Institute of Biological Sciences, Beijing, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.1 kDa 
• Atom Count: 1,921 
• Modeled Residue Count: 237 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-4	A	280	Homo sapiens	Mutation(s): 1  Gene Names: CASP4 EC: 3.4.22.57
UniProt & NIH Common Fund Data Resources
Find proteins for P49662 (Homo sapiens) Explore P49662  Go to UniProtKB:  P49662
PHAROS:  P49662 GTEx:  ENSG00000196954

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.571	α = 90
b = 77.571	β = 90
c = 85.82	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Hou, Y.J., Zeng, H., Shao, F., Ding, J.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2023-02-01
  Changes: Database references
• Version 1.2: 2023-03-29
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description