[English] 日本語
Yorodumi
- PDB-6kmv: caspase-11 C254A P22/P10 in complex with mouse GSDMD-C domain -

+
Open data


ID or keywords:

Loading...

-
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 / Regulation of TLR by endogenous ligand / Interleukin-1 processing / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / pore complex assembly ...caspase-11 / Release of apoptotic factors from the mitochondria / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / Pyroptosis / Regulation of TLR by endogenous ligand / Interleukin-1 processing / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / pore complex assembly / AIM2 inflammasome complex / IPAF inflammasome complex / NLRP1 inflammasome complex / : / wide pore channel activity / NLRP3 inflammasome complex / NOD1/2 Signaling Pathway / caspase binding / cardiolipin binding / phosphatidic acid binding / phosphatidylinositol-4-phosphate binding / positive regulation of macrophage cytokine production / positive regulation of NLRP3 inflammasome complex assembly / phosphatidylserine binding / pyroptotic inflammatory response / 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 / mitochondrial membrane / lipopolysaccharide binding / actin filament organization / 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 / inflammatory response / 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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more