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- PDB-23bd: Caspase-4 p22/p10 and human GSDMD complex -

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Basic information

Entry
Database: PDB / ID: 23bd
TitleCaspase-4 p22/p10 and human GSDMD complex
Components
  • (Caspase-4) x 2
  • Gasdermin-D
KeywordsIMMUNE SYSTEM / Caspase-4 / Gasdermin D / Cryo-EM / Interdomain linker
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLuan, Y. / Mao, Y.D.
Funding support China, 1items
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, E.B. / Mao, Y.D.
History
DepositionJan 30, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 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

Downloads & links

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Assembly

Deposited unit
B: Caspase-4
E: Caspase-4
C: Caspase-4
D: Caspase-4
A: Gasdermin-D


Theoretical massNumber of molelcules
Total (without water)115,8185
Polymers115,8185
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 Caspase-4 / Caspase-4 p22 / CASP-4 / ICE and Ced-3 homolog 2 / ICH-2 / ICE(rel)-II / Mih1 / Protease TX


Mass: 20987.738 Da / Num. of mol.: 2 / Mutation: C258A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP4, ICH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): ClearColi / References: UniProt: P49662, caspase-4
#2: Protein Caspase-4 / CASP-4 / ICE and Ced-3 homolog 2 / ICH-2 / ICE(rel)-II / Mih1 / Protease TX


Mass: 10423.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP4, ICH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): ClearColi / References: UniProt: P49662, caspase-4
#3: Protein Gasdermin-D / Gasdermin domain-containing protein 1


Mass: 52994.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSDMD, DFNA5L, GSDMDC1, FKSG10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P57764
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: Structure of caspase-4 p22/p10 in complex with gasdermin D
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.113 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.22 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: OTHER

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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: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.21.2_5419model refinement
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 695026 / 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_d0.0037197
ELECTRON MICROSCOPYf_angle_d0.5449743
ELECTRON MICROSCOPYf_dihedral_angle_d4.855957
ELECTRON MICROSCOPYf_chiral_restr0.0391095
ELECTRON MICROSCOPYf_plane_restr0.0041264

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