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- EMDB-64739: Cryo-EM structure of Runella bGSDM pore -

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Basic information

Entry
Database: EMDB / ID: EMD-64739
TitleCryo-EM structure of Runella bGSDM pore
Map data
Sample
  • Complex: Runella bGSDM pore
    • Protein or peptide: Gasdermin bGSDM, N-terminus
Keywordsgasdermin pore / ANTIMICROBIAL PROTEIN
Function / homology: / Bacterial Gasdermin Family / defense response to virus / plasma membrane / cytoplasm / Gasdermin bGSDM
Function and homology information
Biological speciesRunella zeae DSM 19591 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsSu Z / Feng Y / Gan JH / Feng YJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Runella bGSDM pore
Authors: Feng YJ / Gan JH / Feng Y / Su Z
History
DepositionMay 20, 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_64739.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 600 pix.
= 720. Å		1.2 Å/pix.
x 600 pix.
= 720. Å		1.2 Å/pix.
x 600 pix.
= 720. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-1.2211373 - 1.8967673
Average (Standard dev.)0.0043562814 (±0.038764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 720.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64739_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_64739_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 : Runella bGSDM pore

EntireName: Runella bGSDM pore
Components
  • Complex: Runella bGSDM pore
    • Protein or peptide: Gasdermin bGSDM, N-terminus

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Supramolecule #1: Runella bGSDM pore

SupramoleculeName: Runella bGSDM pore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Runella zeae DSM 19591 (bacteria)

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Macromolecule #1: Gasdermin bGSDM, N-terminus

MacromoleculeName: Gasdermin bGSDM, N-terminus / type: protein_or_peptide / ID: 1 / Number of copies: 92 / Enantiomer: LEVO
Source (natural)Organism: Runella zeae DSM 19591 (bacteria)
Molecular weightTheoretical: 27.480336 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PFVVALKDKG YSLVAYPKTS IRPLHIYEHT IKNAFKRIWI QSEAQPTSGF IKSLFSDKIH GAIGLSDGQG IDIDLRKTNS LSSAVAAKI LESYFQDSAP SFDLAFENSS SVIFHIEEII TTDADEISLR NWLNDNQNEL REIYKEEIKK GNFFVATSLL R AKKMRMQF ...String:
PFVVALKDKG YSLVAYPKTS IRPLHIYEHT IKNAFKRIWI QSEAQPTSGF IKSLFSDKIH GAIGLSDGQG IDIDLRKTNS LSSAVAAKI LESYFQDSAP SFDLAFENSS SVIFHIEEII TTDADEISLR NWLNDNQNEL REIYKEEIKK GNFFVATSLL R AKKMRMQF ERKNKGELGV DVSKIKNLPV DAKLESKIEG STYDRLVFET PDEGIVFGVK LVRLFFSDNG ILTIDKKQDF NR VL

UniProtKB: Gasdermin bGSDM

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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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: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 528881
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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