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- PDB-7wr1: P32 of caspase-4 C258A mutant in complex with OspC3 C-terminal an... -

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Basic information

Entry
Database: PDB / ID: 7wr1
TitleP32 of caspase-4 C258A mutant in complex with OspC3 C-terminal ankyrin-repeat domain
Components
  • Caspase-4
  • OspC3
KeywordsTRANSFERASE / ADP-riboxanase / effector / ankyrin-repeat domain
Function / homology
Function and homology information


symbiont-mediated suppression of host signal transduction pathway / symbiont-mediated suppression of host calcium-mediated signal transduction / caspase-4 / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / symbiont-mediated suppression of host programmed cell death / non-canonical inflammasome complex assembly / symbiont-mediated perturbation of host programmed cell death ...symbiont-mediated suppression of host signal transduction pathway / symbiont-mediated suppression of host calcium-mediated signal transduction / caspase-4 / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / symbiont-mediated suppression of host programmed cell death / non-canonical inflammasome complex assembly / symbiont-mediated perturbation of host programmed cell death / NLRP1 inflammasome complex / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / pyroptotic inflammatory response / protein autoprocessing / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / intrinsic apoptotic signaling pathway / protein maturation / lipopolysaccharide binding / NOD1/2 Signaling Pathway / cellular response to amyloid-beta / positive regulation of inflammatory response / positive regulation of neuron apoptotic process / toxin activity / regulation of inflammatory response / host cell cytoplasm / calmodulin binding / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / cysteine-type endopeptidase activity / apoptotic process / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / proteolysis / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / Caspase recruitment domain / 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. ...Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / Caspase recruitment domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Caspase-4 / Arginine ADP-riboxanase OspC3
Similarity search - Component
Biological speciesHomo sapiens (human)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsHou, Y.J. / Zeng, H. / Shao, F. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
Title: Structural mechanisms of calmodulin activation of Shigella effector OspC3 to ADP-riboxanate caspase-4/11 and block pyroptosis.
Authors: Hou, Y. / Zeng, H. / Li, Z. / Feng, N. / Meng, F. / Xu, Y. / Li, L. / Shao, F. / Ding, J.
History
DepositionJan 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: OspC3
D: OspC3


Theoretical massNumber of molelcules
Total (without water)100,9234
Polymers100,9234
Non-polymers00
Water9,152508
1
A: Caspase-4


Theoretical massNumber of molelcules
Total (without water)32,0951
Polymers32,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Caspase-4


Theoretical massNumber of molelcules
Total (without water)32,0951
Polymers32,0951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: OspC3


Theoretical massNumber of molelcules
Total (without water)18,3661
Polymers18,3661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: OspC3


Theoretical massNumber of molelcules
Total (without water)18,3661
Polymers18,3661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.639, 59.751, 121.746
Angle α, β, γ (deg.)90.000, 104.083, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Caspase-4 / CASP-4


Mass: 32095.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP4 / Plasmid: pET28a-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49662, caspase-4
#2: Protein OspC3


Mass: 18366.213 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ospC3 / Plasmid: pGEX-6p-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R4X5L7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5% PEG8000, 0.1M Tris-HCl pH 7.5, % 2-propanol

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.13→46.58 Å / Num. obs: 59327 / % possible obs: 98.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.078 / Net I/σ(I): 17.83
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 5.77 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.04 / Num. unique obs: 3988 / CC1/2: 0.901 / Rrim(I) all: 0.492 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WR0

7wr0


Resolution: 2.13→46.57 Å / SU ML: 0.2164 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2496
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1999 2001 3.37 %
Rwork0.1704 57317 -
obs0.1714 59318 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.07 Å2
Refinement stepCycle: LAST / Resolution: 2.13→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6085 0 0 508 6593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00356192
X-RAY DIFFRACTIONf_angle_d0.59498324
X-RAY DIFFRACTIONf_chiral_restr0.0422920
X-RAY DIFFRACTIONf_plane_restr0.00331071
X-RAY DIFFRACTIONf_dihedral_angle_d20.51852358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.190.28151180.22643710X-RAY DIFFRACTION90.45
2.19-2.240.25661430.20014026X-RAY DIFFRACTION98.4
2.24-2.310.24451520.19554107X-RAY DIFFRACTION99.21
2.31-2.380.21961290.18434085X-RAY DIFFRACTION99.41
2.38-2.470.24511510.18414083X-RAY DIFFRACTION99.44
2.47-2.570.22241440.18734092X-RAY DIFFRACTION99.46
2.57-2.690.2281310.18864102X-RAY DIFFRACTION99.62
2.69-2.830.22121540.18794130X-RAY DIFFRACTION99.51
2.83-30.2181480.194104X-RAY DIFFRACTION99.7
3-3.240.21251330.18744149X-RAY DIFFRACTION99.86
3.24-3.560.20941470.17614119X-RAY DIFFRACTION99.86
3.56-4.080.17851540.14764161X-RAY DIFFRACTION99.88
4.08-5.140.15881410.13534194X-RAY DIFFRACTION99.88
5.14-46.570.17221560.16344255X-RAY DIFFRACTION99.48

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