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

Validation slider image for 9H5M

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

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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View more in-depth experimental data

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

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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.