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- PDB-6kmu: P22/P10 complex of caspase-11 mutant C254A -

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Basic information

Entry
Database: PDB / ID: 6kmu
TitleP22/P10 complex of caspase-11 mutant C254A
Components(Caspase-4) x 5
KeywordsIMMUNE SYSTEM / pyroptosis
Function / homology
Function and homology information


caspase-11 / non-canonical inflammasome complex / Pyroptosis / positive regulation of interleukin-18-mediated signaling pathway / pyroptotic cell death / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / canonical inflammasome complex / NOD1/2 Signaling Pathway / positive regulation of macrophage cytokine production ...caspase-11 / non-canonical inflammasome complex / Pyroptosis / positive regulation of interleukin-18-mediated signaling pathway / pyroptotic cell death / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / canonical inflammasome complex / NOD1/2 Signaling Pathway / positive regulation of macrophage cytokine production / pyroptotic inflammatory response / positive regulation of NLRP3 inflammasome complex assembly / protein autoprocessing / ectopic germ cell programmed cell death / actin filament organization / protein maturation / positive regulation of interleukin-1 beta production / lipopolysaccharide binding / positive regulation of inflammatory response / regulation of inflammatory response / regulation of apoptotic process / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / cysteine-type endopeptidase activity / lipid binding / endoplasmic reticulum membrane / mitochondrion / extracellular region / cytosol / cytoplasm
Similarity search - Function
Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 ...Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / 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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
C: Caspase-4
D: Caspase-4
E: Caspase-4
F: Caspase-4
G: Caspase-4
H: Caspase-4


Theoretical massNumber of molelcules
Total (without water)120,4148
Polymers120,4148
Non-polymers00
Water6,557364
1
A: Caspase-4
B: Caspase-4


Theoretical massNumber of molelcules
Total (without water)30,8972
Polymers30,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-32 kcal/mol
Surface area12730 Å2
MethodPISA
2
C: Caspase-4
D: Caspase-4


Theoretical massNumber of molelcules
Total (without water)31,0982
Polymers31,0982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-28 kcal/mol
Surface area12760 Å2
MethodPISA
3
E: Caspase-4
F: Caspase-4


Theoretical massNumber of molelcules
Total (without water)30,8972
Polymers30,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-30 kcal/mol
Surface area12180 Å2
MethodPISA
4
G: Caspase-4
H: Caspase-4


Theoretical massNumber of molelcules
Total (without water)27,5222
Polymers27,5222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-29 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.971, 102.002, 99.744
Angle α, β, γ (deg.)90.00, 93.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 5 types, 8 molecules AEBFHCDG

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


Mass: 20783.809 Da / Num. of mol.: 2 / 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: 10113.619 Da / Num. of mol.: 3
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: 20884.914 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: 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
#5: Protein Caspase-4 / CASP-4 / Caspase-11 / CASP-11 / Protease ICH-3


Mass: 17408.006 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

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Non-polymers , 1 types, 364 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES (pH 7.5), 12% (w/v) polyethylene glycol 3350, and 4% formaldehyde

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.1→49.78 Å / Num. obs: 71527 / % possible obs: 97.7 % / Redundancy: 3.41 % / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.81
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 5274 / CC1/2: 0.915

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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: 6kmt

6kmt


Resolution: 2.1→49.78 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2511 2019 -
Rwork0.2097 --
obs0.2109 71422 98.76 %
Refinement stepCycle: LAST / Resolution: 2.1→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8041 0 0 364 8405
LS refinement shellResolution: 2.0994→2.1519 Å
RfactorNum. reflection% reflection
Rfree0.3505 --
Rwork0.2878 --
obs-5070 99 %

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