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- PDB-6kn1: P20/P12 of caspase-11 mutant C254A -

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Basic information

Entry
Database: PDB / ID: 6kn1
TitleP20/P12 of caspase-11 mutant C254A
Components(Caspase-4) x 4
KeywordsIMMUNE SYSTEM / pyroptosis
Function / homology
Function and homology information


caspase-11 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / Pyroptosis / pyroptotic cell death / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / NLRP1 inflammasome complex / NOD1/2 Signaling Pathway / positive regulation of macrophage cytokine production ...caspase-11 / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / Pyroptosis / pyroptotic cell death / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / NLRP1 inflammasome complex / NOD1/2 Signaling Pathway / positive regulation of macrophage cytokine production / positive regulation of NLRP3 inflammasome complex assembly / pyroptotic inflammatory response / protein autoprocessing / protein maturation / ectopic germ cell programmed cell death / positive regulation of interleukin-1 beta production / actin filament organization / lipopolysaccharide binding / positive regulation of inflammatory response / positive regulation of neuron apoptotic process / regulation of inflammatory response / scaffold protein binding / defense response to Gram-positive bacterium / defense response to bacterium / cysteine-type endopeptidase activity / innate immune response / neuronal cell body / lipid binding / endoplasmic reticulum membrane / protein-containing complex / mitochondrion / extracellular region / cytosol / cytoplasm
Similarity search - Function
Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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 recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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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
C: Caspase-4
D: Caspase-4


Theoretical massNumber of molelcules
Total (without water)56,5454
Polymers56,5454
Non-polymers00
Water5,873326
1
A: Caspase-4
B: Caspase-4


Theoretical massNumber of molelcules
Total (without water)28,7662
Polymers28,7662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-26 kcal/mol
Surface area12630 Å2
MethodPISA
2
C: Caspase-4
D: Caspase-4


Theoretical massNumber of molelcules
Total (without water)27,7792
Polymers27,7792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-25 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.001, 99.941, 58.294
Angle α, β, γ (deg.)90.00, 114.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Caspase-4 / CASP-4 / Caspase-11 / CASP-11 / Protease ICH-3


Mass: 18553.299 Da / Num. of mol.: 1 / Mutation: C254A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Casp4, Casp11, Caspl, Ich3 / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70343, caspase-11
#2: Protein Caspase-4 / CASP-4 / Caspase-11 / CASP-11 / Protease ICH-3


Mass: 10212.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Casp4, Casp11, Caspl, Ich3 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70343, caspase-11
#3: Protein Caspase-4 / CASP-4 / Caspase-11 / CASP-11 / Protease ICH-3


Mass: 17495.045 Da / Num. of mol.: 1 / Mutation: C254A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Casp4, Casp11, Caspl, Ich3 / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70343, caspase-11
#4: Protein Caspase-4 / CASP-4 / Caspase-11 / CASP-11 / Protease ICH-3


Mass: 10283.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Casp4, Casp11, Caspl, Ich3 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70343, caspase-11
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate pH 5.7 and 18% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→46.89 Å / Num. obs: 42565 / % possible obs: 98.9 % / Redundancy: 3.47 % / CC1/2: 0.996 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.2
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.93 / Num. unique obs: 3036 / CC1/2: 0.941 / % possible all: 95.1

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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: 1.9→46.89 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2175 1993 -
Rwork0.1875 --
obs0.189 42522 99.06 %
Refinement stepCycle: LAST / Resolution: 1.9→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3962 0 0 326 4288
LS refinement shellResolution: 1.9→1.9445 Å
RfactorNum. reflection% reflection
Rfree0.3151 --
Rwork0.2463 --
obs-2919 95 %

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