7WJQ | pdb_00007wjq

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.252 (Depositor), 0.256 (DCC)
R-Value Work:
0.210 (Depositor), 0.211 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7WJQ

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18014
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TAX9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.252 (Depositor), 0.256 (DCC)
R-Value Work: 0.210 (Depositor), 0.211 (DCC)
R-Value Observed: 0.212 (Depositor)

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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	--

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.