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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
TitleCrystal structure of Chromobacterium violaceum effector CopC in complex with host calmodulin and caspase-7
Components
  • Calmodulin-1
  • Caspase-7
  • CopC
KeywordsTRANSFERASE
Function / homology
Function and homology information


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 / : / 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 / : / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / fibroblast 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 / 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 / execution phase of apoptosis / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / 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 / Apoptotic cleavage of cellular proteins / 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 / 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 / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / Smooth Muscle Contraction / regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / Caspase-mediated cleavage of cytoskeletal proteins / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / eNOS activation / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / response to UV / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / cysteine-type peptidase activity / 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 / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / regulation of cytokinesis / 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 / RAF activation / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity
Similarity search - Function
Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / Ankyrin repeat / 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 ...Arginine ADP-riboxanase OspC1-3 / Shigella flexneri OspC protein / Ankyrin repeat / 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 / : / EF-hand domain pair / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Ankyrin repeat / EF-hand, calcium binding motif / Ankyrin repeat-containing domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-1 / Caspase-7 / Arginine ADP-riboxanase CopC
Similarity search - Component
Biological speciesChromobacterium violaceum ATCC 12472 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsDing, J.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29020202 China
CitationJournal: Mbio / Year: 2022
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
DepositionFeb 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 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: CopC
B: Caspase-7
C: Calmodulin-1


Theoretical massNumber of molelcules
Total (without water)98,7533
Polymers98,7533
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-24 kcal/mol
Surface area32980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.871, 90.871, 426.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CopC


Mass: 48446.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum ATCC 12472 (bacteria)
Strain: ATCC 12472 / Gene: CV_2038 / Plasmid: pGEX6p-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7NWF2
#2: Protein Caspase-7 / CASP-7


Mass: 33055.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P55210, caspase-7
#3: Protein Calmodulin-1


Mass: 17250.984 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: pSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0DP23

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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: 4.45 Å3/Da / Density % sol: 72.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Bis-Tris propane pH 7.5, 1.5 M lithium sulfate

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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 PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K88

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
RfactorNum. reflection% reflection
Rfree0.3137 1990 9.13 %
Rwork0.2743 --
obs0.2779 21794 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5515 0 0 0 5515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0015630
X-RAY DIFFRACTIONf_angle_d0.3527584
X-RAY DIFFRACTIONf_dihedral_angle_d10.6632048
X-RAY DIFFRACTIONf_chiral_restr0.036805
X-RAY DIFFRACTIONf_plane_restr0.003999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.690.47121380.43161373X-RAY DIFFRACTION99
3.69-3.790.47861380.37461387X-RAY DIFFRACTION99
3.79-3.90.3791350.32781360X-RAY DIFFRACTION99
3.9-4.020.38741380.31281368X-RAY DIFFRACTION100
4.02-4.170.34071400.29081388X-RAY DIFFRACTION100
4.17-4.330.31681410.27291402X-RAY DIFFRACTION100
4.33-4.530.25871410.26131385X-RAY DIFFRACTION100
4.53-4.770.26231380.2551394X-RAY DIFFRACTION99
4.77-5.070.3391420.25771411X-RAY DIFFRACTION100
5.07-5.460.35121420.29471401X-RAY DIFFRACTION100
5.46-6.010.3271440.30881425X-RAY DIFFRACTION100
6.01-6.880.33371440.29251431X-RAY DIFFRACTION100
6.88-8.650.26561490.25221478X-RAY DIFFRACTION100
8.65-47.650.29661600.2471601X-RAY DIFFRACTION100

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