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- PDB-6kmz: caspase-4 P22/P10 C258A in complex with human GSDMD-C domain -

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Basic information

Entry
Database: PDB / ID: 6kmz
Titlecaspase-4 P22/P10 C258A in complex with human GSDMD-C domain
Components
  • (Caspase-4) x 2
  • (Gasdermin-D) x 2
KeywordsIMMUNE SYSTEM / pyroptosis
Function / homology
Function and homology information


caspase-4 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / non-canonical inflammasome complex assembly / pore complex assembly / AIM2 inflammasome complex / IPAF inflammasome complex / NLRP1 inflammasome complex / : / Release of apoptotic factors from the mitochondria ...caspase-4 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / non-canonical inflammasome complex assembly / pore complex assembly / AIM2 inflammasome complex / IPAF inflammasome complex / NLRP1 inflammasome complex / : / Release of apoptotic factors from the mitochondria / wide pore channel activity / NLRP3 inflammasome complex / CARD domain binding / caspase binding / cardiolipin binding / Regulation of TLR by endogenous ligand / phosphatidic acid binding / positive regulation of tumor necrosis factor-mediated signaling pathway / Interleukin-1 processing / phosphatidylinositol-4-phosphate binding / phosphatidylserine binding / pyroptotic inflammatory response / protein autoprocessing / protein maturation / protein secretion / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / Purinergic signaling in leishmaniasis infection / phosphatidylinositol-4,5-bisphosphate binding / intrinsic apoptotic signaling pathway / positive regulation of interleukin-1 beta production / mitochondrial membrane / lipopolysaccharide binding / NOD1/2 Signaling Pathway / protein homooligomerization / positive regulation of inflammatory response / specific granule lumen / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / tertiary granule lumen / regulation of inflammatory response / defense response to Gram-negative bacterium / ficolin-1-rich granule lumen / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / cysteine-type endopeptidase activity / innate immune response / lipid binding / apoptotic process / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / proteolysis / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 ...Gasdermin, PUB domain / Gasdermin PUB domain / Gasdermin, pore forming domain / Gasdermin pore forming domain / Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / 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-4 / Gasdermin-D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.61 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 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-4
B: Caspase-4
E: Gasdermin-D
C: Caspase-4
D: Caspase-4
H: Gasdermin-D
a: Caspase-4
b: Caspase-4
c: Caspase-4
d: Caspase-4


Theoretical massNumber of molelcules
Total (without water)167,27810
Polymers167,27810
Non-polymers00
Water00
1
A: Caspase-4
B: Caspase-4
E: Gasdermin-D
a: Caspase-4
b: Caspase-4


Theoretical massNumber of molelcules
Total (without water)83,5815
Polymers83,5815
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Caspase-4
D: Caspase-4
H: Gasdermin-D
c: Caspase-4
d: Caspase-4


Theoretical massNumber of molelcules
Total (without water)83,6965
Polymers83,6965
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.568, 140.568, 329.355
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein
Caspase-4 / CASP-4 / ICE and Ced-3 homolog 2 / ICH-2 / ICE(rel)-II / Mih1 / Protease TX


Mass: 20987.738 Da / Num. of mol.: 4 / Mutation: C258A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP4, ICH2 / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49662, caspase-4
#2: Protein Gasdermin-D / Gasdermin domain-containing protein 1


Mass: 20757.803 Da / Num. of mol.: 1
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
#3: Protein Gasdermin-D / Gasdermin domain-containing protein 1


Mass: 20872.891 Da / Num. of mol.: 1
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
#4: 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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP4, ICH2 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49662, caspase-4

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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: 5.32 Å3/Da / Density % sol: 76.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl pH 7.5, 200 mM sodium tartrate, 20% (w/v) polyethylene glycol 3350, 5% glycerol and 4% 1,1,1,3,3,3-hexafluoro-2-propanol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 3.61→49.14 Å / Num. obs: 38808 / % possible obs: 99.5 % / Redundancy: 6.43 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.83
Reflection shellResolution: 3.61→3.7 Å / Rmerge(I) obs: 1.106 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2781 / CC1/2: 0.768 / % possible all: 97.7

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Processing

Software
NameClassificationNB
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KMU

6kmu


Resolution: 3.61→45.48 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.3191 1993 -1993
Rwork0.3112 ---
obs0.3116 38742 97 %-
Refinement stepCycle: LAST / Resolution: 3.61→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10693 0 0 0 10693
LS refinement shellResolution: 3.61→3.73 Å
RfactorNum. reflection% reflection
Rfree0.3974 --
Rwork0.3369 3537 -
obs--97.7 %

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