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- PDB-7wr6: Crystal structure of ADP-riboxanated caspase-4 in complex with Af1521 -

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Basic information

Entry
Database: PDB / ID: 7wr6
TitleCrystal structure of ADP-riboxanated caspase-4 in complex with Af1521
Components
  • ADP-ribose glycohydrolase AF_1521
  • Caspase-4Caspase 4
KeywordsHYDROLASE / ADP-riboxanation
Function / homology
Function and homology information


caspase-4 / non-canonical inflammasome complex / ADP-ribosylglutamate hydrolase activity / positive regulation of interleukin-18-mediated signaling pathway / peptidyl-glutamate ADP-deribosylation / non-canonical inflammasome complex assembly / canonical inflammasome complex / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis ...caspase-4 / non-canonical inflammasome complex / ADP-ribosylglutamate hydrolase activity / positive regulation of interleukin-18-mediated signaling pathway / peptidyl-glutamate ADP-deribosylation / non-canonical inflammasome complex assembly / canonical inflammasome complex / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / pyroptotic inflammatory response / protein maturation / protein autoprocessing / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / intrinsic apoptotic signaling pathway / lipopolysaccharide binding / NOD1/2 Signaling Pathway / positive regulation of inflammatory response / cellular response to amyloid-beta / regulation of inflammatory response / regulation of apoptotic process / defense response to Gram-positive bacterium / defense response to bacterium / inflammatory response / cysteine-type endopeptidase activity / innate immune response / apoptotic process / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / proteolysis / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Caspase recruitment domain / 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. ...Caspase recruitment domain / 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 / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like
Similarity search - Domain/homology
Chem-5ZY / ADP-ribose glycohydrolase AF_1521 / Caspase-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Archaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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

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Assembly

Deposited unit
A: Caspase-4
B: ADP-ribose glycohydrolase AF_1521
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4843
Polymers53,8012
Non-polymers6821
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-3 kcal/mol
Surface area20120 Å2
Unit cell
Length a, b, c (Å)42.143, 59.920, 187.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Caspase-4 / Caspase 4 / CASP-4 / ICE and Ced-3 homolog 2 / ICH-2 / ICE(rel)-II / Mih1 / Protease TX


Mass: 32095.428 Da / Num. of mol.: 1 / Mutation: C258A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP4, ICH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49662, caspase-4
#2: Protein ADP-ribose glycohydrolase AF_1521 / [Protein ADP-ribosylaspartate] hydrolase AF_1521 / [Protein ADP-ribosylglutamate] hydrolase AF_1521


Mass: 21706.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea)
Strain: ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16
Gene: AF_1521 / Plasmid: pGEX-6p-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O28751, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#3: Chemical ChemComp-5ZY / [[(3~{a}~{S},5~{R},6~{R},6~{a}~{R})-2-azanylidene-3-[(4~{R})-4-azanyl-5-oxidanylidene-pentyl]-6-oxidanyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxazol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 682.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32N8O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 27% PEG 3350, 0.05M CAPSO pH 9.0

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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: 1.96→38.45 Å / Num. obs: 34358 / % possible obs: 97.7 % / Redundancy: 12.88 % / Biso Wilson estimate: 34.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.064 / Net I/σ(I): 24.49
Reflection shellResolution: 1.96→2.01 Å / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 3.92 / Num. unique obs: 2364 / CC1/2: 0.936 / Rrim(I) all: 0.69 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BFQ, 7WR0

2bfq

7wr0


Resolution: 1.96→38.45 Å / SU ML: 0.2302 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.7199
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2283 1999 5.83 %
Rwork0.1962 32296 -
obs0.198 34295 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.7 Å2
Refinement stepCycle: LAST / Resolution: 1.96→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 0 189 3720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253610
X-RAY DIFFRACTIONf_angle_d0.51394876
X-RAY DIFFRACTIONf_chiral_restr0.0432541
X-RAY DIFFRACTIONf_plane_restr0.0034621
X-RAY DIFFRACTIONf_dihedral_angle_d26.611355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.25171320.25772147X-RAY DIFFRACTION91.6
2.01-2.070.30031400.24382275X-RAY DIFFRACTION99.02
2.07-2.130.2951390.23322238X-RAY DIFFRACTION96.31
2.13-2.190.28571410.22292267X-RAY DIFFRACTION98.33
2.19-2.270.25551410.22572280X-RAY DIFFRACTION98.14
2.27-2.360.25241410.2282285X-RAY DIFFRACTION97
2.36-2.470.2941430.20752284X-RAY DIFFRACTION98.22
2.47-2.60.24651420.21742321X-RAY DIFFRACTION99.23
2.6-2.760.2471430.20472298X-RAY DIFFRACTION98.43
2.77-2.980.25811440.21192326X-RAY DIFFRACTION98.25
2.98-3.280.24971440.20962311X-RAY DIFFRACTION98.2
3.28-3.750.20821460.18672360X-RAY DIFFRACTION98.86
3.75-4.730.18561490.16752408X-RAY DIFFRACTION99.11
4.73-38.450.20221540.17722496X-RAY DIFFRACTION98

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