7WJQ

Crystal structure of GSDMB in complex with Ipah7.8

• PDB DOI: https://doi.org/10.2210/pdb7WJQ/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Shigella flexneri, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-01-07 Released: 2023-01-11 
• Deposition Author(s): Li, X., Zhang, H., Yin, H.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.252 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Literature

Insights into the GSDMB-mediated cellular lysis and its targeting by IpaH7.8

Yin, H., Zheng, J., He, Q., Zhang, X., Li, X., Ma, Y., Liang, X., Gao, J., Kocsis, B.L., Li, Z., Liu, X., Alto, N.M., Li, L., Zhang, H.

(2023) Nat Commun 14: 61

• DOI: https://doi.org/10.1038/s41467-022-35725-0

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 72.38 kDa 
• Atom Count: 4,555 
• Modelled Residue Count: 568 
• Deposited Residue Count: 631 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable E3 ubiquitin-protein ligase ipaH7.8	A	242	Shigella flexneri	Mutation(s): 1  EC: 2.3.2.27
UniProt
Find proteins for P18014 (Shigella flexneri) Explore P18014  Go to UniProtKB:  P18014

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Gasdermin-B	B	389	Homo sapiens	Mutation(s): 2  Gene Names: GSDMB, GSDML, PP4052, PRO2521
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAX9 (Homo sapiens) Explore Q8TAX9  Go to UniProtKB:  Q8TAX9
PHAROS:  Q8TAX9 GTEx:  ENSG00000073605

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.252 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.471	α = 90
b = 87.584	β = 90
c = 102.794	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-11 
Deposition Author(s): Li, X., Zhang, H., Yin, H.

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Funding Organization	Location	Grant Number
Other government	China	--

Revision History  

• Version 1.0: 2023-01-11
  Type: Initial release
  
• Version 1.1: 2023-07-05
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description