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- PDB-9v2s: Cryo-EM structure of Runella bGSDM pore -

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Basic information

Entry
Database: PDB / ID: 9v2s
TitleCryo-EM structure of Runella bGSDM pore
ComponentsGasdermin bGSDM, N-terminus
KeywordsANTIMICROBIAL PROTEIN / gasdermin pore
Function / homology: / Bacterial Gasdermin Family / defense response to virus / plasma membrane / cytoplasm / Gasdermin bGSDM
Function and homology information
Biological speciesRunella zeae DSM 19591 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsSu, Z. / Feng, Y. / Gan, J.H. / Feng, Y.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Runella bGSDM pore
Authors: Feng, Y.J. / Gan, J.H. / Feng, Y. / Su, Z.
History
DepositionMay 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gasdermin bGSDM, N-terminus
B: Gasdermin bGSDM, N-terminus
C: Gasdermin bGSDM, N-terminus
D: Gasdermin bGSDM, N-terminus
E: Gasdermin bGSDM, N-terminus
F: Gasdermin bGSDM, N-terminus
G: Gasdermin bGSDM, N-terminus
H: Gasdermin bGSDM, N-terminus
I: Gasdermin bGSDM, N-terminus
J: Gasdermin bGSDM, N-terminus
K: Gasdermin bGSDM, N-terminus
L: Gasdermin bGSDM, N-terminus
M: Gasdermin bGSDM, N-terminus
N: Gasdermin bGSDM, N-terminus
O: Gasdermin bGSDM, N-terminus
P: Gasdermin bGSDM, N-terminus
Q: Gasdermin bGSDM, N-terminus
R: Gasdermin bGSDM, N-terminus
S: Gasdermin bGSDM, N-terminus
T: Gasdermin bGSDM, N-terminus
U: Gasdermin bGSDM, N-terminus
V: Gasdermin bGSDM, N-terminus
W: Gasdermin bGSDM, N-terminus
X: Gasdermin bGSDM, N-terminus
Y: Gasdermin bGSDM, N-terminus
Z: Gasdermin bGSDM, N-terminus
a: Gasdermin bGSDM, N-terminus
b: Gasdermin bGSDM, N-terminus
c: Gasdermin bGSDM, N-terminus
d: Gasdermin bGSDM, N-terminus
e: Gasdermin bGSDM, N-terminus
f: Gasdermin bGSDM, N-terminus
g: Gasdermin bGSDM, N-terminus
h: Gasdermin bGSDM, N-terminus
i: Gasdermin bGSDM, N-terminus
j: Gasdermin bGSDM, N-terminus
k: Gasdermin bGSDM, N-terminus
l: Gasdermin bGSDM, N-terminus
m: Gasdermin bGSDM, N-terminus
n: Gasdermin bGSDM, N-terminus
o: Gasdermin bGSDM, N-terminus
p: Gasdermin bGSDM, N-terminus
q: Gasdermin bGSDM, N-terminus
r: Gasdermin bGSDM, N-terminus
s: Gasdermin bGSDM, N-terminus
t: Gasdermin bGSDM, N-terminus
u: Gasdermin bGSDM, N-terminus
v: Gasdermin bGSDM, N-terminus
w: Gasdermin bGSDM, N-terminus
x: Gasdermin bGSDM, N-terminus
y: Gasdermin bGSDM, N-terminus
z: Gasdermin bGSDM, N-terminus
1: Gasdermin bGSDM, N-terminus
2: Gasdermin bGSDM, N-terminus
3: Gasdermin bGSDM, N-terminus
4: Gasdermin bGSDM, N-terminus
5: Gasdermin bGSDM, N-terminus
6: Gasdermin bGSDM, N-terminus
7: Gasdermin bGSDM, N-terminus
8: Gasdermin bGSDM, N-terminus
9: Gasdermin bGSDM, N-terminus
0: Gasdermin bGSDM, N-terminus
AA: Gasdermin bGSDM, N-terminus
AB: Gasdermin bGSDM, N-terminus
AC: Gasdermin bGSDM, N-terminus
AD: Gasdermin bGSDM, N-terminus
AE: Gasdermin bGSDM, N-terminus
AF: Gasdermin bGSDM, N-terminus
AG: Gasdermin bGSDM, N-terminus
AH: Gasdermin bGSDM, N-terminus
AI: Gasdermin bGSDM, N-terminus
AJ: Gasdermin bGSDM, N-terminus
AK: Gasdermin bGSDM, N-terminus
AL: Gasdermin bGSDM, N-terminus
AM: Gasdermin bGSDM, N-terminus
AN: Gasdermin bGSDM, N-terminus
AO: Gasdermin bGSDM, N-terminus
AP: Gasdermin bGSDM, N-terminus
AQ: Gasdermin bGSDM, N-terminus
AR: Gasdermin bGSDM, N-terminus
AS: Gasdermin bGSDM, N-terminus
AT: Gasdermin bGSDM, N-terminus
AU: Gasdermin bGSDM, N-terminus
AV: Gasdermin bGSDM, N-terminus
AW: Gasdermin bGSDM, N-terminus
AX: Gasdermin bGSDM, N-terminus
AY: Gasdermin bGSDM, N-terminus
AZ: Gasdermin bGSDM, N-terminus
Aa: Gasdermin bGSDM, N-terminus
Ab: Gasdermin bGSDM, N-terminus
Ac: Gasdermin bGSDM, N-terminus
Ad: Gasdermin bGSDM, N-terminus


Theoretical massNumber of molelcules
Total (without water)2,528,19192
Polymers2,528,19192
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Gasdermin bGSDM, N-terminus


Mass: 27480.336 Da / Num. of mol.: 92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Runella zeae DSM 19591 (bacteria) / Gene: G563DRAFT_02010 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DV48
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Runella bGSDM pore / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Runella zeae DSM 19591 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DIFFRACTION / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 528881 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 14.15 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0057164680
ELECTRON MICROSCOPYf_angle_d0.7526220984
ELECTRON MICROSCOPYf_chiral_restr0.050324932
ELECTRON MICROSCOPYf_plane_restr0.004427876
ELECTRON MICROSCOPYf_dihedral_angle_d6.00521344

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