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- PDB-7wzs: Crystal structure of Chromobacterium violaceum effector CopC in c... -
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Basic information
Entry | Database: PDB / ID: 7wzs | ||||||
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Title | Crystal structure of Chromobacterium violaceum effector CopC in complex with host calmodulin and caspase-7 | ||||||
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![]() | TRANSFERASE | ||||||
Function / homology | ![]() Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / caspase-7 / symbiont-mediated perturbation of host programmed cell death / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage ...Lyases; Carbon-nitrogen lyases; Other carbon-nitrogen lyases / ADP-riboxanase activity / caspase-7 / symbiont-mediated perturbation of host programmed cell death / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / fibroblast apoptotic process / execution phase of apoptosis / Reduction of cytosolic Ca++ levels / 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 / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Apoptotic cleavage of cellular proteins / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / protein maturation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / Caspase-mediated cleavage of cytoskeletal proteins / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to UV / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of protein dephosphorylation / Ion homeostasis / cysteine-type peptidase activity / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / striated muscle cell differentiation / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / protein catabolic process / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ding, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Calmodulin Binding Activates Chromobacterium CopC Effector to ADP-Riboxanate Host Apoptotic Caspases. Authors: Liu, Y. / Zeng, H. / Hou, Y. / Li, Z. / Li, L. / Song, X. / Ding, J. / Shao, F. / Xu, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.2 KB | Display | ![]() |
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PDB format | ![]() | 118.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.1 KB | Display | ![]() |
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Full document | ![]() | 458.2 KB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k88S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48446.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 12472 / Gene: CV_2038 / Plasmid: pGEX6p-2 / Production host: ![]() ![]() |
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#2: Protein | Mass: 33055.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 17250.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.45 Å3/Da / Density % sol: 72.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM Bis-Tris propane pH 7.5, 1.5 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→47.65 Å / Num. obs: 21855 / % possible obs: 99.9 % / Redundancy: 8.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 3.6→3.69 Å / Redundancy: 8 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1562 / CC1/2: 0.838 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1K88 Resolution: 3.6→47.65 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→47.65 Å
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Refine LS restraints |
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LS refinement shell |
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