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- PDB-6kmv: caspase-11 C254A P22/P10 in complex with mouse GSDMD-C domain -

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Basic information

Entry
Database: PDB / ID: 6kmv
Titlecaspase-11 C254A P22/P10 in complex with mouse GSDMD-C domain
Components
  • (Caspase-4) x 9
  • (Gasdermin-D) x 6
KeywordsIMMUNE SYSTEM / pyroptosis
Function / homology
Function and homology information


caspase-11 / Release of apoptotic factors from the mitochondria / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / Pyroptosis / pyroptotic cell death / Regulation of TLR by endogenous ligand / Interleukin-1 processing / non-canonical inflammasome complex assembly / detection of lipopolysaccharide ...caspase-11 / Release of apoptotic factors from the mitochondria / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / Pyroptosis / pyroptotic cell death / Regulation of TLR by endogenous ligand / Interleukin-1 processing / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / pore complex assembly / NLRP1 inflammasome complex / NLRP3 inflammasome complex / wide pore channel activity / NOD1/2 Signaling Pathway / phosphatidic acid binding / cardiolipin binding / phosphatidylinositol-4-phosphate binding / positive regulation of macrophage cytokine production / positive regulation of NLRP3 inflammasome complex assembly / pyroptotic inflammatory response / phosphatidylserine binding / protein autoprocessing / protein maturation / protein secretion / ectopic germ cell programmed cell death / phosphatidylinositol-4,5-bisphosphate binding / Neutrophil degranulation / positive regulation of interleukin-1 beta production / actin filament organization / lipopolysaccharide binding / mitochondrial membrane / protein homooligomerization / positive regulation of inflammatory response / positive regulation of neuron apoptotic process / regulation of inflammatory response / scaffold protein binding / defense response to Gram-negative bacterium / 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 space / extracellular region / nucleoplasm / plasma membrane / cytosol / cytoplasm
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 / Peptidase family C14A, His active site ...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 / 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
Caspase-4 / Gasdermin-D
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 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: Gasdermin-D
D: Gasdermin-D
E: Caspase-4
F: Caspase-4
G: Gasdermin-D
H: Gasdermin-D
I: Caspase-4
J: Caspase-4
K: Gasdermin-D
L: Gasdermin-D
M: Caspase-4
N: Caspase-4
O: Gasdermin-D
P: Gasdermin-D
Q: Caspase-4
R: Caspase-4
S: Gasdermin-D
T: Gasdermin-D
U: Caspase-4
V: Caspase-4
W: Gasdermin-D
X: Gasdermin-D
Y: Caspase-4
Z: Caspase-4
a: Gasdermin-D
b: Gasdermin-D
c: Caspase-4
d: Caspase-4
e: Gasdermin-D
f: Gasdermin-D
g: Caspase-4
h: Caspase-4
i: Caspase-4
j: Caspase-4
k: Caspase-4
l: Caspase-4
m: Caspase-4
n: Caspase-4
o: Caspase-4
p: Caspase-4
q: Caspase-4
r: Caspase-4
s: Caspase-4
t: Caspase-4
u: Caspase-4
v: Caspase-4


Theoretical massNumber of molelcules
Total (without water)805,58548
Polymers805,58548
Non-polymers00
Water00
1
A: Caspase-4
C: Gasdermin-D
g: Caspase-4


Theoretical massNumber of molelcules
Total (without water)49,8123
Polymers49,8123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Caspase-4
D: Gasdermin-D
h: Caspase-4


Theoretical massNumber of molelcules
Total (without water)50,5813
Polymers50,5813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Caspase-4
G: Gasdermin-D
i: Caspase-4


Theoretical massNumber of molelcules
Total (without water)50,5653
Polymers50,5653
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Caspase-4
H: Gasdermin-D
j: Caspase-4


Theoretical massNumber of molelcules
Total (without water)49,7703
Polymers49,7703
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Caspase-4
K: Gasdermin-D
k: Caspase-4


Theoretical massNumber of molelcules
Total (without water)50,3933
Polymers50,3933
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
J: Caspase-4
L: Gasdermin-D
l: Caspase-4


Theoretical massNumber of molelcules
Total (without water)50,2533
Polymers50,2533
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Caspase-4
O: Gasdermin-D
m: Caspase-4


Theoretical massNumber of molelcules
Total (without water)50,4643
Polymers50,4643
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
N: Caspase-4
P: Gasdermin-D
n: Caspase-4


Theoretical massNumber of molelcules
Total (without water)52,1923
Polymers52,1923
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
Q: Caspase-4
S: Gasdermin-D
o: Caspase-4


Theoretical massNumber of molelcules
Total (without water)50,3933
Polymers50,3933
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
R: Caspase-4
T: Gasdermin-D
p: Caspase-4


Theoretical massNumber of molelcules
Total (without water)48,5413
Polymers48,5413
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
U: Caspase-4
W: Gasdermin-D
q: Caspase-4


Theoretical massNumber of molelcules
Total (without water)50,3653
Polymers50,3653
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
V: Caspase-4
X: Gasdermin-D
r: Caspase-4


Theoretical massNumber of molelcules
Total (without water)50,7233
Polymers50,7233
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
Y: Caspase-4
a: Gasdermin-D
s: Caspase-4


Theoretical massNumber of molelcules
Total (without water)50,2073
Polymers50,2073
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
Z: Caspase-4
b: Gasdermin-D
t: Caspase-4


Theoretical massNumber of molelcules
Total (without water)50,4943
Polymers50,4943
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
c: Caspase-4
e: Gasdermin-D
u: Caspase-4


Theoretical massNumber of molelcules
Total (without water)50,3403
Polymers50,3403
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
d: Caspase-4
f: Gasdermin-D
v: Caspase-4


Theoretical massNumber of molelcules
Total (without water)50,4943
Polymers50,4943
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.798, 139.207, 175.942
Angle α, β, γ (deg.)92.43, 99.06, 96.35
Int Tables number1
Space group name H-MP1

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Components

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Protein , 15 types, 48 molecules ABVCGODKSTWbfEFZdHIMNQYJLPeRcU...

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


Mass: 18030.602 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: 18870.598 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
#3: Protein Gasdermin-D / Gasdermin domain-containing protein 1


Mass: 21497.508 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsdmdc1, Gsdmd / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9D8T2
#4: Protein
Gasdermin-D / Gasdermin domain-containing protein 1


Mass: 21426.430 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsdmdc1, Gsdmd / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9D8T2
#5: Protein
Caspase-4 / CASP-4 / Caspase-11 / CASP-11 / Protease ICH-3


Mass: 18783.520 Da / Num. of mol.: 4 / 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
#6: Protein Gasdermin-D / Gasdermin domain-containing protein 1


Mass: 20702.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsdmdc1, Gsdmd / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9D8T2
#7: Protein
Caspase-4 / CASP-4 / Caspase-11 / CASP-11 / Protease ICH-3


Mass: 18682.414 Da / Num. of mol.: 5 / 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
#8: Protein Caspase-4 / CASP-4 / Caspase-11 / CASP-11 / Protease ICH-3


Mass: 16744.094 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
#9: Protein Gasdermin-D / Gasdermin domain-containing protein 1


Mass: 23225.375 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsdmdc1, Gsdmd / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9D8T2
#10: Protein Caspase-4 / CASP-4 / Caspase-11 / CASP-11 / Protease ICH-3


Mass: 16831.172 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
#11: Protein Caspase-4 / CASP-4 / Caspase-11 / CASP-11 / Protease ICH-3


Mass: 18654.406 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
#12: Protein Gasdermin-D / Gasdermin domain-containing protein 1


Mass: 21568.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsdmdc1, Gsdmd / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9D8T2
#13: Protein Gasdermin-D / Gasdermin domain-containing protein 1


Mass: 21311.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsdmdc1, Gsdmd / Plasmid: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9D8T2
#14: Protein
Caspase-4 / CASP-4 / Caspase-11 / CASP-11 / Protease ICH-3


Mass: 10283.828 Da / Num. of mol.: 15
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
#15: 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: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70343, caspase-11

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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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium malonate (pH 6.5), 18% polyethylene glycol 3350, and 10 mM TCEP

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 3.35→45.07 Å / Num. obs: 118363 / % possible obs: 98.3 % / Redundancy: 3.41 % / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.1
Reflection shellResolution: 3.35→3.43 Å / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.23 / Num. unique obs: 8903 / CC1/2: 0.771

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Processing

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

6kmu


Resolution: 3.35→37.442 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1999 -1999
Rwork0.2188 ---
obs0.2194 118238 98.24 %-
Refinement stepCycle: LAST / Resolution: 3.35→37.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56064 0 0 0 56064
LS refinement shellResolution: 3.35→3.43 Å
RfactorNum. reflection% reflection
Rfree0.3196 --
Rwork0.3105 8142 -
obs--95 %

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