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- EMDB-64528: Cryo-EM structures of fGSDM/HET-Q1 pores -

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Basic information

Entry
Database: EMDB / ID: EMD-64528
TitleCryo-EM structures of fGSDM/HET-Q1 pores
Map data
Sample
  • Complex: fGSDM/HET-Q1 pores
    • Protein or peptide: fGSDM/HET-Q1 pores
KeywordsPyroptosis / gasdermin / ANTIMICROBIAL PROTEIN
Biological speciesPodospora anserina (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsSu Z / Feng Y / Gan JH / Feng YJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2023YFC2307100 China
CitationJournal: To Be Published
Title: Cryo-EM structures of fGSDM/HET-Q1 pores
Authors: Su Z / Feng YJ
History
DepositionMay 9, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64528.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.8806925 - 2.211127
Average (Standard dev.)0.001712789 (±0.06518561)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64528_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_64528_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 : fGSDM/HET-Q1 pores

EntireName: fGSDM/HET-Q1 pores
Components
  • Complex: fGSDM/HET-Q1 pores
    • Protein or peptide: fGSDM/HET-Q1 pores

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Supramolecule #1: fGSDM/HET-Q1 pores

SupramoleculeName: fGSDM/HET-Q1 pores / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Podospora anserina (fungus)

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Macromolecule #1: fGSDM/HET-Q1 pores

MacromoleculeName: fGSDM/HET-Q1 pores / type: protein_or_peptide / ID: 1 / Number of copies: 40 / Enantiomer: LEVO
Source (natural)Organism: Podospora anserina (fungus)
Molecular weightTheoretical: 24.962373 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QHAFAGSERW VVPRYSSKPG TLIRLGSVLT DPEDLESSLN LDSIPPIPPN LLRDATPEVR MSVQTELSKS DSTLAKAAPA LEGILTLGG GVEASRSQGV SSSLNISGTV KATVFRADKS YMDVLLKDKN VISYAKRGLG KPMFVVVGVA TAGRVEMKET R HATRKAGV ...String:
QHAFAGSERW VVPRYSSKPG TLIRLGSVLT DPEDLESSLN LDSIPPIPPN LLRDATPEVR MSVQTELSKS DSTLAKAAPA LEGILTLGG GVEASRSQGV SSSLNISGTV KATVFRADKS YMDVLLKDKN VISYAKRGLG KPMFVVVGVA TAGRVEMKET R HATRKAGV SGKVGVEVIG EGEVGLERER SDKSCNEVRG EGGLDFAYRV REFGYSRVRG TVKDKGDWTG KVLF

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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

Concentration3 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 651337
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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