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Yorodumi- PDB-7wr5: Crystal structure of OspC3-calmodulin-caspase-4 complex binding w... -
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-Basic information
Entry | Database: PDB / ID: 7wr5 | ||||||
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Title | Crystal structure of OspC3-calmodulin-caspase-4 complex binding with 2'-aF-NAD+ | ||||||
Components |
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Keywords | TRANSFERASE / ADP-riboxanase / effector | ||||||
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 / symbiont-mediated suppression of host programmed cell death / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / NLRP1 inflammasome complex ...symbiont-mediated suppression of host signal transduction pathway / : / symbiont-mediated suppression of host calcium-mediated signal transduction / caspase-4 / symbiont-mediated suppression of host programmed cell death / Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / non-canonical inflammasome complex / positive regulation of interleukin-18-mediated signaling pathway / NLRP1 inflammasome complex / symbiont-mediated perturbation of host programmed cell death / non-canonical inflammasome complex assembly / CARD domain binding / positive regulation of tumor necrosis factor-mediated signaling pathway / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / Calmodulin induced events / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / organelle localization by membrane tethering / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / pyroptotic inflammatory response / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / adenylate cyclase activator activity / protein phosphatase activator activity / RHO GTPases activate PAKs / Ion transport by P-type ATPases / : / protein maturation / Uptake and function of anthrax toxins / Long-term potentiation / protein autoprocessing / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / catalytic complex / DARPP-32 events / regulation of cardiac muscle contraction / detection of calcium ion / Pyroptosis / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / cellular response to interferon-beta / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / eNOS activation / Protein methylation / voltage-gated potassium channel complex / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / Ion homeostasis / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / calcium channel complex / substantia nigra development / Ras activation upon Ca2+ influx through NMDA receptor / intrinsic apoptotic signaling pathway / sarcomere / regulation of heart rate / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / VEGFR2 mediated cell proliferation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of peptidyl-threonine phosphorylation / spindle microtubule / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / lipopolysaccharide binding / RAF activation / NOD1/2 Signaling Pathway / Transcriptional activation of mitochondrial biogenesis Similarity search - Function | ||||||
Biological species | Shigella flexneri (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Hou, Y.J. / Zeng, H. / Shao, F. / Ding, J. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wr5.cif.gz | 215.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wr5.ent.gz | 136.5 KB | Display | PDB format |
PDBx/mmJSON format | 7wr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wr5_validation.pdf.gz | 740.3 KB | Display | wwPDB validaton report |
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Full document | 7wr5_full_validation.pdf.gz | 750.2 KB | Display | |
Data in XML | 7wr5_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 7wr5_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/7wr5 ftp://data.pdbj.org/pub/pdb/validation_reports/wr/7wr5 | HTTPS FTP |
-Related structure data
Related structure data | 7wr0C 7wr1C 7wr2C 7wr3C 7wr4SC 7wr6C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49705.074 Da / Num. of mol.: 1 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) / Strain (production host): BL21(DE3) / References: UniProt: R4X5L7 |
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#2: Protein | Mass: 16852.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0DP23 |
#3: Protein | 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 / Plasmid: pET28a-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49662, caspase-4 |
#4: Chemical | ChemComp-5ZV / [[( |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M Potassium acetate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→49.07 Å / Num. obs: 16826 / % possible obs: 99.7 % / Redundancy: 12.8 % / Biso Wilson estimate: 82.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Rrim(I) all: 0.167 / Net I/σ(I): 14.98 |
Reflection shell | Resolution: 3.1→3.18 Å / Rmerge(I) obs: 1.388 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 1194 / CC1/2: 0.746 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WR4 Resolution: 3.1→49.07 Å / SU ML: 0.499 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.5961 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→49.07 Å
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Refine LS restraints |
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LS refinement shell |
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