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- EMDB-71549: CryoEM structure of the GSDME pore, C27 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71549
TitleCryoEM structure of the GSDME pore, C27
Map dataGSDME pore, C27 symmetry
Sample
  • Complex: GSDME
    • Protein or peptide: Gasdermin-E, N-terminal
KeywordsPore-forming protein / Innate immunity / Pyroptosis / Tumor immunity / IMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of immune response to tumor cell / pyroptotic cell death / Release of apoptotic factors from the mitochondria / inner ear auditory receptor cell differentiation / wide pore channel activity / Regulation of TLR by endogenous ligand / programmed cell death / cardiolipin binding / Pyroptosis / pyroptotic inflammatory response ...positive regulation of immune response to tumor cell / pyroptotic cell death / Release of apoptotic factors from the mitochondria / inner ear auditory receptor cell differentiation / wide pore channel activity / Regulation of TLR by endogenous ligand / programmed cell death / cardiolipin binding / Pyroptosis / pyroptotic inflammatory response / positive regulation of intrinsic apoptotic signaling pathway / phosphatidylinositol-4,5-bisphosphate binding / Defective pyroptosis / sensory perception of sound / cellular response to virus / cellular response to tumor necrosis factor / positive regulation of MAPK cascade / negative regulation of cell population proliferation / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Gasdermin-E / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsTeran E / Ni DC / Wang CW / Ruan JB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: CryoEM structure of the GSDME pore, C27 symmetry
Authors: Teran E / Ni DC / Wang CW / Ruan JB
History
DepositionJul 1, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71549.png

Downloads & links

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Map

FileDownload / File: emd_71549.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGSDME pore, C27 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 480 pix.
= 444.48 Å		0.93 Å/pix.
x 480 pix.
= 444.48 Å		0.93 Å/pix.
x 480 pix.
= 444.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.926 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.065
Minimum - Maximum-0.09331804 - 0.3452755
Average (Standard dev.)0.0013256667 (±0.011705533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 444.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: GSDME pore, C27 symmetry, half 1

Fileemd_71549_half_map_1.map
AnnotationGSDME pore, C27 symmetry, half 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GSDME pore, C27 symmetry, half 2

Fileemd_71549_half_map_2.map
AnnotationGSDME pore, C27 symmetry, half 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GSDME

EntireName: GSDME
Components
  • Complex: GSDME
    • Protein or peptide: Gasdermin-E, N-terminal

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Supramolecule #1: GSDME

SupramoleculeName: GSDME / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gasdermin-E, N-terminal

MacromoleculeName: Gasdermin-E, N-terminal / type: protein_or_peptide / ID: 1 / Number of copies: 27 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.366771 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFAKATRNFL REVDADGDLI AVSNLNDSDK LQLLSLVTKK KRFWCWQRPK YQFLSLTLGD VLIEDQFPSP VVVESDFVKY EGKFANHVS GTLETALGKV KLNLGGSSRV ESQSSFGTLR KQEVDLQQLI RDSAERTINL RNPVLQQVLE GRNEVLCVLT Q KITTMQKC ...String:
MFAKATRNFL REVDADGDLI AVSNLNDSDK LQLLSLVTKK KRFWCWQRPK YQFLSLTLGD VLIEDQFPSP VVVESDFVKY EGKFANHVS GTLETALGKV KLNLGGSSRV ESQSSFGTLR KQEVDLQQLI RDSAERTINL RNPVLQQVLE GRNEVLCVLT Q KITTMQKC VISEHMQVEE KCGGIVGIQT KTVQVSATED GNVTKDSNVV LEIPAATTIA YGVIELYVKL DAQFEFCLLR GK QGGFENK KRIDSVYLDP LVFREFAFID MPD

UniProtKB: Gasdermin-E

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C27 (27 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Number images used: 17305
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9pe0:
CryoEM structure of the GSDME pore, C27

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