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- PDB-6paw: Crystal structure of DAPK2 S308A Calcium/Calmodulin complex -

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Basic information

Entry
Database: PDB / ID: 6paw
TitleCrystal structure of DAPK2 S308A Calcium/Calmodulin complex
Components
  • Calmodulin-1
  • Death-associated protein kinase 2
KeywordsTRANSFERASE / APOPTOSIS / Kinase / Calcium signaling / Autophagy / Homodimer / Complex
Function / homology
Function and homology information


autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / positive regulation of eosinophil chemotaxis / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of neutrophil chemotaxis / anoikis / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events ...autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / positive regulation of eosinophil chemotaxis / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of neutrophil chemotaxis / anoikis / 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) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / Activation of RAC1 downstream of NMDARs / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / autophagosome membrane docking / 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 / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / 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 / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of protein dephosphorylation / voltage-gated potassium channel complex / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / positive regulation of protein autophosphorylation / sperm midpiece / 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 / regulation of autophagy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / Transcriptional activation of mitochondrial biogenesis / positive regulation of protein serine/threonine kinase activity / spindle microtubule / Stimuli-sensing channels / cellular response to type II interferon / spindle pole / response to calcium ion / RAS processing / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Inactivation, recovery and regulation of the phototransduction cascade / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Platelet degranulation
Similarity search - Function
EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Calmodulin-1 / Death-associated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.953 Å
AuthorsSimon, B. / Wilmanns, M.
CitationJournal: To Be Published
Title: Crystal structure of Death-associated protein kinase 2 in complex with Calcium Calmodulin
Authors: Simon, B. / Wilmanns, M.
History
DepositionJun 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Death-associated protein kinase 2
B: Death-associated protein kinase 2
D: Calmodulin-1
E: Death-associated protein kinase 2
F: Death-associated protein kinase 2
G: Calmodulin-1
H: Calmodulin-1
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,27417
Polymers216,9138
Non-polymers3619
Water0
1
A: Death-associated protein kinase 2
D: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3896
Polymers54,2282
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-52 kcal/mol
Surface area23010 Å2
MethodPISA
2
B: Death-associated protein kinase 2
C: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3084
Polymers54,2282
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-45 kcal/mol
Surface area20690 Å2
MethodPISA
3
E: Death-associated protein kinase 2
H: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2683
Polymers54,2282
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-9 kcal/mol
Surface area19680 Å2
MethodPISA
4
F: Death-associated protein kinase 2
G: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3084
Polymers54,2282
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-39 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.440, 95.880, 263.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Death-associated protein kinase 2 / DAP kinase 2 / DAP-kinase-related protein 1 / DRP-1


Mass: 37375.727 Da / Num. of mol.: 4 / Mutation: S308A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK2 / Plasmid: pnEK / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9UIK4, non-specific serine/threonine protein kinase
#2: Protein
Calmodulin-1 /


Mass: 16852.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Plasmid: pnEK / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DP23
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris-HCl, pH 6.5, 0.6 M sodium chloride, 14.3% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.95→131.65 Å / Num. obs: 48427 / % possible obs: 64.4 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.275 / Net I/σ(I): 9.5
Reflection shellResolution: 2.95→3.2 Å / Rmerge(I) obs: 1.853 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1250

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALENovember 3, 2014 BUILT=20141118data scaling
PDB_EXTRACT3.25data extraction
XDSNovember 3, 2014data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2A2A & 1ZUZ

2a2a

1zuz


Resolution: 2.953→131.65 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.61
RfactorNum. reflection% reflection
Rfree0.2884 1575 5.05 %
Rwork0.2486 --
obs0.2506 31216 64.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.8 Å2 / Biso mean: 57.7375 Å2 / Biso min: 12.11 Å2
Refinement stepCycle: final / Resolution: 2.953→131.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12979 0 9 0 12988
Biso mean--77.89 --
Num. residues----1596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9528-3.04810.55590.34771471564
3.0481-3.15710.3341300.356744047011
3.1571-3.28350.3163470.345783688320
3.2835-3.43290.3283840.32251416150034
3.4329-3.61390.36521220.29172402252458
3.6139-3.84040.33251720.24893292346479
3.8404-4.13690.30751990.22174047424697
4.1369-4.55320.26362190.218941824401100
4.5532-5.21210.27682230.227541974420100
5.2121-6.56670.29272180.264942644482100
6.5667-131.7810.25782520.258344184670100

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