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- EMDB-67181: CryoEM structure of hGZMA-hGSDMB -

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Basic information

Entry
Database: EMDB / ID: EMD-67181
TitleCryoEM structure of hGZMA-hGSDMB
Map data
Sample
  • Complex: CryoEM structure of hGZMA-hGSDMB
    • Protein or peptide: Granzyme A
    • Protein or peptide: Gasdermin-B
KeywordsGranzyme A / Gasdermin B. / IMMUNE SYSTEM
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhao X / Zhang K / Liu Z
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: CryoEM structure of hGZMA-hGSDMB
Authors: Zhao X / Zhang K / Liu Z
History
DepositionNov 21, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67181.png

Downloads & links

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Map

FileDownload / File: emd_67181.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.20084168 - 0.40800288
Average (Standard dev.)-0.00016302758 (±0.009279833)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 275.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_67181_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67181_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67181_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 : CryoEM structure of hGZMA-hGSDMB

EntireName: CryoEM structure of hGZMA-hGSDMB
Components
  • Complex: CryoEM structure of hGZMA-hGSDMB
    • Protein or peptide: Granzyme A
    • Protein or peptide: Gasdermin-B

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Supramolecule #1: CryoEM structure of hGZMA-hGSDMB

SupramoleculeName: CryoEM structure of hGZMA-hGSDMB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Granzyme A

MacromoleculeName: Granzyme A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: granzyme A
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.985363 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: IIGGNEVTPH SRPYMVLLSL DRKTICAGAL IAKDWVLTAA HCNLNKRSQV ILGAHSITRE EPTKQIMLVK KEFPYPCYDP ATREGDLKL LQLMEKAKIN KYVTILHLPK KGDDVKPGTM CQVAGWGRTH NSASWSDTLR EVNITIIDRK VCNDRNHYNF N PVIGMNMV ...String:
IIGGNEVTPH SRPYMVLLSL DRKTICAGAL IAKDWVLTAA HCNLNKRSQV ILGAHSITRE EPTKQIMLVK KEFPYPCYDP ATREGDLKL LQLMEKAKIN KYVTILHLPK KGDDVKPGTM CQVAGWGRTH NSASWSDTLR EVNITIIDRK VCNDRNHYNF N PVIGMNMV CAGSLRGGRD SCNGDAGSPL LCEGVFRGVT SFGLENKCGD PRGPGVYILL SKKHLNWIIM TIKGAVGKTH HH HHH

UniProtKB: Granzyme A

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Macromolecule #2: Gasdermin-B

MacromoleculeName: Gasdermin-B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.497941 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMFSVFEEIT RIVVKEMDAG GDMIAVRSLV DADRFRCFHL VGEKRTFFGC RHYTTGLTLM DILDTDGDKW LDELDSGLQG QKAEFQILD NVDSTGELIV RLPKEITISG SFQGFHHQKI KISENRISQQ YLATLENRKL KRELPFSFRS INTRENLYLV T ETLETVKE ...String:
SMFSVFEEIT RIVVKEMDAG GDMIAVRSLV DADRFRCFHL VGEKRTFFGC RHYTTGLTLM DILDTDGDKW LDELDSGLQG QKAEFQILD NVDSTGELIV RLPKEITISG SFQGFHHQKI KISENRISQQ YLATLENRKL KRELPFSFRS INTRENLYLV T ETLETVKE ETLKSDRQYK FWSQISQGHL SYKHKGQREV TIPPNRVLSY RVKQLVFPNK ETMNIHFRGK TKSFPEEKDG AS SCLGKSL GSEDSRNMKE KLEDMESVLK DLTEEKRKDV LNSLAKCLGK EDIRQDLEQR VSEVLISGEL HMEDPDKPLL SSL FNAAGV LVEARAKAIL DFLDALLELS EEQQFVAEAL EKGTLPLLKD QVKSVMEQNW DELASSPPDM DYDPEARILC ALYV VVSIL LELAEGPTSV SS

UniProtKB: Gasdermin-B

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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: GATAN K3 (6k x 4k) / Average electron dose: 1.74 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 147609
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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