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- EMDB-68823: Caspase-4 p20/p10 and human GSDMD -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-68823
TitleCaspase-4 p20/p10 and human GSDMD
Map data
Sample
  • Complex: Caspase-4 p20/p10 and GSDMD complex
    • Protein or peptide: Caspase-4
    • Protein or peptide: Caspase-4
    • Protein or peptide: Gasdermin-D
KeywordsCaspase-4 / Gasdermin D / Cryo-EM / Interdomain linker / IMMUNE SYSTEM
Function / homology
Function and homology information


caspase-4 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / pyroptotic cell death / non-canonical inflammasome complex assembly / NLRP1 inflammasome complex / Release of apoptotic factors from the mitochondria / CARD domain binding / pore complex assembly / NLRP3 inflammasome complex ...caspase-4 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / pyroptotic cell death / non-canonical inflammasome complex assembly / NLRP1 inflammasome complex / Release of apoptotic factors from the mitochondria / CARD domain binding / pore complex assembly / NLRP3 inflammasome complex / wide pore channel activity / Regulation of TLR by endogenous ligand / Interleukin-1 processing / phosphatidic acid binding / plasma membrane repair / positive regulation of tumor necrosis factor-mediated signaling pathway / cardiolipin binding / phosphatidylinositol-4-phosphate binding / ceramide biosynthetic process / phosphatidylserine binding / protein autoprocessing / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / protein secretion / pyroptotic inflammatory response / Pyroptosis / Purinergic signaling in leishmaniasis infection / phosphatidylinositol-4,5-bisphosphate binding / intrinsic apoptotic signaling pathway / positive regulation of interleukin-1 beta production / lipopolysaccharide binding / protein maturation / NOD1/2 Signaling Pathway / protein homooligomerization / specific granule lumen / mitochondrial membrane / cellular response to amyloid-beta / positive regulation of inflammatory response / tertiary granule lumen / positive regulation of neuron apoptotic process / regulation of inflammatory response / ficolin-1-rich granule lumen / defense response to Gram-negative bacterium / defense response to bacterium / defense response to Gram-positive bacterium / innate immune response / cysteine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / proteolysis / : / extracellular region / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Gasdermin / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family ...Gasdermin / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily
Similarity search - Domain/homology
Caspase-4 / Gasdermin-D
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLuan Y / Mao YD
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11774012 China
CitationJournal: Structure / Year: 2026
Title: Cryo-EM structures of human caspase-4 in complex with full-length gasdermin D
Authors: Luan Y / Chen EB / Mao YD
History
DepositionJan 30, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68823.png

Downloads & links

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Map

FileDownload / File: emd_68823.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å		0.85 Å/pix.
x 300 pix.
= 255. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00612
Minimum - Maximum-0.015856827 - 0.04213884
Average (Standard dev.)0.0000662438 (±0.0012247211)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 255.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_68823_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_68823_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_68823_half_map_2.map
Projections & Slices
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Sample components

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Entire : Caspase-4 p20/p10 and GSDMD complex

EntireName: Caspase-4 p20/p10 and GSDMD complex
Components
  • Complex: Caspase-4 p20/p10 and GSDMD complex
    • Protein or peptide: Caspase-4
    • Protein or peptide: Caspase-4
    • Protein or peptide: Gasdermin-D

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Supramolecule #1: Caspase-4 p20/p10 and GSDMD complex

SupramoleculeName: Caspase-4 p20/p10 and GSDMD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 113 KDa

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Macromolecule #1: Caspase-4

MacromoleculeName: Caspase-4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: caspase-4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.026771 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
ALKLCPHEEF LRLCKERAEE IYPIKERNNR TRLALIICNT EFDHLPPRNG ADFDITGMKE LLEGLDYSVD VEENLTARDM ESALRAFAT RPEHKSSDST FLVLMSHGIL EGICGTVHDE KKPDVLLYDT IFQIFNNRNC LSLKDKPKVI IVQAARGANR G ELWVRD

UniProtKB: Caspase-4

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Macromolecule #2: Caspase-4

MacromoleculeName: Caspase-4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: caspase-4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.423982 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
AVYKTHVEKD FIAFCSSTPH NVSWRDSTMG SIFITQLITC FQKYSWCCHL EEVFRKVQQS FETPRAKAQM PTIERLSMTR YFYLFPGN

UniProtKB: Caspase-4

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Macromolecule #3: Gasdermin-D

MacromoleculeName: Gasdermin-D / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.851777 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSAFERVVR RVVQELDHGG EFIPVTSLQS STGFQPYCLV VRKPSSSWFW KPRYKCVNLS IKDILEPDAA EPDVQRGRSF HFYDAMDGQ IQGSVELAAP GQAKIAGGAA VSDSSSTSMN VYSLSVDPNT WQTLLHERHL RQPEHKVLQQ LRSRGDNVYV V TEVLQTQK ...String:
MGSAFERVVR RVVQELDHGG EFIPVTSLQS STGFQPYCLV VRKPSSSWFW KPRYKCVNLS IKDILEPDAA EPDVQRGRSF HFYDAMDGQ IQGSVELAAP GQAKIAGGAA VSDSSSTSMN VYSLSVDPNT WQTLLHERHL RQPEHKVLQQ LRSRGDNVYV V TEVLQTQK EVEVTRTHKR EGSGRFSLPG ATCLQGEGQG HLSQKKTVTI PSGSTLAFRV AQLVIDSDLD VLLFPDKKQR TF QPPATGH KRSTSEGAWP QLPSGLSMMR CLHNFLTDGV PAEGAFTEDF QGLRAEVETI SKELELLDRE LCQLLLEGLE GVL RDQLAL RALEEALEQG QSLGPVEPLD GPAGAVLECL VLSSGMLVPE LAIPVVYLLG ALTMLSETQH KLLAEALESQ TLLG PLELV GSLLEQSAPW QERSTMSLPP GLLGNSWGEG APAWVLLDEC GLELGEDTPH VCWEPQAQGR MCALYASLAL LSGLS QEPH

UniProtKB: Gasdermin-D

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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

Concentration0.22 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 594428
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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