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- EMDB-51889: Cryo-EM structure of Gasdermin-E -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51889
TitleCryo-EM structure of Gasdermin-E
Map data
Sample
  • Complex: GasderminE
    • Protein or peptide: Gasdermin-E, N-terminal
KeywordsPore forming protein / APOPTOSIS
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 / pyroptotic inflammatory response / Pyroptosis ...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 / pyroptotic inflammatory response / Pyroptosis / 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: 3.6 Å
AuthorsYildiz O / Garcia-Saez AJ / Shalaby R
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Structural mechanism of Gasdermin E-mediated mtDNA release from apoptotic mitochondria
Authors: Yildiz O / Garcia-Saez AJ / Shalaby R
History
DepositionOct 22, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51889.png

Downloads & links

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Map

FileDownload / File: emd_51889.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 500 pix.
= 418.5 Å		0.84 Å/pix.
x 500 pix.
= 418.5 Å		0.84 Å/pix.
x 500 pix.
= 418.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.26863652 - 0.4864343
Average (Standard dev.)0.0010366084 (±0.0146162575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 418.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51889_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51889_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GasderminE

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

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Supramolecule #1: GasderminE

SupramoleculeName: GasderminE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: GasderminE
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30 KDa

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Macromolecule #1: Gasdermin-E, N-terminal

MacromoleculeName: Gasdermin-E, N-terminal / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.337273 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 DGQFEFCLLR GK QGGFE

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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 273073
CTF correctionSoftware - Name: cryoSPARC (ver. 2.6) / Type: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C30 (30 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.6) / Number images used: 88579
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.6)
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

jsr4


Chain - Chain ID: A / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9h5m:
Cryo-EM structure of Gasdermin-E

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