9H5M | pdb_00009h5m

Cryo-EM structure of Gasdermin-E

PDB DOI: https://doi.org/10.2210/pdb9H5M/pdb
EM Map EMD-51889: EMDB EMDataResource

Classification: APOPTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-22 Released: 2025-11-05
Deposition Author(s): Yildiz, O., Garcia-Saez, A.J., Shalaby, R.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural mechanism of Gasdermin E-mediated mtDNA release from apoptotic mitochondria

Yildiz, O., Garcia-Saez, A.J., Shalaby, R.

To be published.

Macromolecule Content

Total Structure Weight: 820.12 kDa
Atom Count: 57,540
Modeled Residue Count: 7,350
Deposited Residue Count: 7,350
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gasdermin-E, N-terminal	A AA [auth a] B BA [auth b] C A, AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	245	Homo sapiens	Mutation(s): 0 Gene Names: GSDME, DFNA5, ICERE1
UniProt & NIH Common Fund Data Resources
Find proteins for O60443 (Homo sapiens) Explore O60443 Go to UniProtKB: O60443
PHAROS: O60443 GTEx: ENSG00000105928
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O60443
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.6

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Garcia-Saez, A.J.

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release

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.