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- PDB-6kn0: caspase-1 P20/P10 C285A in complex with human GSDMD-C domain -

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Basic information

Entry
Database: PDB / ID: 6kn0
Titlecaspase-1 P20/P10 C285A in complex with human GSDMD-C domain
Components
  • (Caspase-1) x 2
  • Gasdermin-D
KeywordsIMMUNE SYSTEM / pyroptosis
Function / homology
Function and homology information


pyroptotic cell death / caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / IPAF inflammasome complex / The AIM2 inflammasome / AIM2 inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex ...pyroptotic cell death / caspase-1 / protease inhibitor complex / AIM2 inflammasome complex assembly / IPAF inflammasome complex / The AIM2 inflammasome / AIM2 inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / NLRP1 inflammasome complex / canonical inflammasome complex / cytokine precursor processing / Release of apoptotic factors from the mitochondria / positive regulation of interleukin-18 production / pore complex assembly / CARD domain binding / NLRP3 inflammasome complex / Regulation of TLR by endogenous ligand / wide pore channel activity / phosphatidic acid binding / Interleukin-1 processing / positive regulation of tumor necrosis factor-mediated signaling pathway / cardiolipin binding / osmosensory signaling pathway / Interleukin-37 signaling / phosphatidylinositol-4-phosphate binding / pattern recognition receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / signaling receptor ligand precursor processing / phosphatidylserine binding / TP53 Regulates Transcription of Caspase Activators and Caspases / cytokine binding / protein autoprocessing / pyroptotic inflammatory response / protein secretion / The NLRP3 inflammasome / Pyroptosis / Purinergic signaling in leishmaniasis infection / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-1 beta production / protein maturation / cellular response to mechanical stimulus / NOD1/2 Signaling Pathway / protein homooligomerization / cellular response to type II interferon / mitochondrial membrane / specific granule lumen / kinase binding / positive regulation of inflammatory response / SARS-CoV-1 activates/modulates innate immune responses / tertiary granule lumen / regulation of inflammatory response / cellular response to lipopolysaccharide / endopeptidase activity / regulation of apoptotic process / defense response to virus / ficolin-1-rich granule lumen / defense response to Gram-negative bacterium / microtubule / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / defense response to Gram-positive bacterium / innate immune response / cysteine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / nucleolus / signal transduction / protein-containing complex / proteolysis / extracellular space / extracellular region / nucleoplasm / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Gasdermin / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Caspase-like / Caspase recruitment domain / Rossmann fold - #1460 / CARD domain / CARD caspase recruitment domain profile. ...Gasdermin / Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Caspase-like / Caspase recruitment domain / Rossmann fold - #1460 / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Caspase-1 / Gasdermin-D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.793 Å
AuthorsDing, J. / Sun, Q.
CitationJournal: Cell / Year: 2020
Title: Structural Mechanism for GSDMD Targeting by Autoprocessed Caspases in Pyroptosis.
Authors: Wang, K. / Sun, Q. / Zhong, X. / Zeng, M. / Zeng, H. / Shi, X. / Li, Z. / Wang, Y. / Zhao, Q. / Shao, F. / Ding, J.
History
DepositionAug 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Mar 12, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-1
B: Caspase-1
C: Caspase-1
D: Caspase-1
E: Gasdermin-D
F: Gasdermin-D


Theoretical massNumber of molelcules
Total (without water)100,5756
Polymers100,5756
Non-polymers00
Water00
1
A: Caspase-1
B: Caspase-1
E: Gasdermin-D


Theoretical massNumber of molelcules
Total (without water)50,2883
Polymers50,2883
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Caspase-1
D: Caspase-1
F: Gasdermin-D


Theoretical massNumber of molelcules
Total (without water)50,2883
Polymers50,2883
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.039, 94.894, 76.081
Angle α, β, γ (deg.)90.00, 116.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Caspase-1 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta- ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta-converting enzyme / p45


Mass: 18778.658 Da / Num. of mol.: 2 / Mutation: C285A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29466, caspase-1
#2: Protein Caspase-1 / CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta- ...CASP-1 / Interleukin-1 beta convertase / IL-1BC / Interleukin-1 beta-converting enzyme / IL-1 beta-converting enzyme / p45


Mass: 10258.755 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP1, IL1BC, IL1BCE / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P29466, caspase-1
#3: Protein Gasdermin-D / Gasdermin domain-containing protein 1


Mass: 21250.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSDMD, DFNA5L, GSDMDC1, FKSG10 / Plasmid: pSUMO / 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 150 mM KBr, 30% (w/v) polyethylene glycol mono-methyester 2000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.79→47.45 Å / Num. obs: 21818 / % possible obs: 97 % / Redundancy: 3.32 % / CC1/2: 0.993 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.2
Reflection shellResolution: 2.79→2.87 Å / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.12 / Num. unique obs: 1526 / CC1/2: 0.876

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KMU

6kmu


Resolution: 2.793→47.447 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2997 1998 -1998
Rwork0.2403 ---
obs0.2457 21811 97.31 %-
Refinement stepCycle: LAST / Resolution: 2.793→47.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6974 0 0 0 6974
LS refinement shellResolution: 2.7931→2.8629 Å
RfactorNum. reflection% reflection
Rfree0.4752 --
Rwork0.3691 --
obs-1471 93 %

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