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- PDB-9xsg: CryoEM structure of hGZMA-hGSDMB -

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Basic information

Entry
Database: PDB / ID: 9xsg
TitleCryoEM structure of hGZMA-hGSDMB
Components
  • Gasdermin-B
  • Granzyme A
KeywordsIMMUNE SYSTEM / Granzyme A / Gasdermin B.
Function / homology
Function and homology information


granzyme A / cytotoxic T cell pyroptotic cell death / granzyme-mediated programmed cell death signaling pathway / cytolytic granule / : / wide pore channel activity / programmed cell death / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding ...granzyme A / cytotoxic T cell pyroptotic cell death / granzyme-mediated programmed cell death signaling pathway / cytolytic granule / : / wide pore channel activity / programmed cell death / cardiolipin binding / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / immunological synapse / pyroptotic inflammatory response / phosphatidylinositol-4,5-bisphosphate binding / protein catabolic process / protein maturation / phospholipid binding / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to bacterium / immune response / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / protein homodimerization activity / proteolysis / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Gasdermin / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family ...Gasdermin / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan
Similarity search - Domain/homology
Granzyme A / Gasdermin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhao, X. / Zhang, K. / Liu, Z.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: CryoEM structure of hGZMA-hGSDMB
Authors: Zhao, X. / Zhang, K. / Liu, Z.
History
DepositionNov 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Granzyme A
B: Granzyme A
E: Gasdermin-B
D: Gasdermin-B


Theoretical massNumber of molelcules
Total (without water)148,9674
Polymers148,9674
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 Granzyme A / CTL tryptase / Cytotoxic T-lymphocyte proteinase 1 / Fragmentin-1 / Granzyme-1 / Hanukkah factor / ...CTL tryptase / Cytotoxic T-lymphocyte proteinase 1 / Fragmentin-1 / Granzyme-1 / Hanukkah factor / H factor / HF


Mass: 26985.363 Da / Num. of mol.: 2 / Mutation: S212A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GZMA, CTLA3, HFSP / Production host: Escherichia coli (E. coli) / References: UniProt: P12544, granzyme A
#2: Protein Gasdermin-B / Gasdermin-like protein


Mass: 47497.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSDMB, GSDML, PP4052, PRO2521 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TAX9
Has protein modificationY

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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: CryoEM structure of hGZMA-hGSDMB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 1.74 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
3EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147609 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037683
ELECTRON MICROSCOPYf_angle_d0.58410359
ELECTRON MICROSCOPYf_dihedral_angle_d4.1811029
ELECTRON MICROSCOPYf_chiral_restr0.0411185
ELECTRON MICROSCOPYf_plane_restr0.0051330

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