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- PDB-6fha: Death-associated Protein Kinase 1 (DAPK1) catalytic and auto-regu... -

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Basic information

Entry
Database: PDB / ID: 6fha
TitleDeath-associated Protein Kinase 1 (DAPK1) catalytic and auto-regulatory domains with S289A and S308A mutations
ComponentsDeath-associated protein kinase 1DAPK1
KeywordsSIGNALING PROTEIN / kinase / apoptosis / autophagy / CaMK
Function / homology
Function and homology information


cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / syntaxin-1 binding / regulation of NMDA receptor activity / calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / syntaxin-1 binding / regulation of NMDA receptor activity / calmodulin-dependent protein kinase activity / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / protein autophosphorylation / postsynaptic density / negative regulation of translation / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / GTP binding / negative regulation of apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHuart, A.-S. / Wilmanns, M.
CitationJournal: To Be Published
Title: Molecular mechanisms behind DAPK regulation: how phosphorylation switches work
Authors: Huart, A.-S. / Simon, B. / Lubner, J. / Mertens, H.D.T. / Temmerman, K. / Hoffmann, J.-E. / Svergun, D.I. / Schwartz, D. / Schultz, C. / Wilmanns, M.
History
DepositionJan 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Death-associated protein kinase 1


Theoretical massNumber of molelcules
Total (without water)38,6471
Polymers38,6471
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.993, 75.820, 93.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Death-associated protein kinase 1 / DAPK1 / DAP kinase 1


Mass: 38647.332 Da / Num. of mol.: 1 / Mutation: S289A S308A
Source method: isolated from a genetically manipulated source
Details: h / Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK1, DAPK / Production host: Escherichia coli (E. coli)
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.4 % / Description: cuboid
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop
Details: 22% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2016 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.878→39.943 Å / Num. obs: 25549 / % possible obs: 91.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 35.977 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.067 / Rrim(I) all: 0.15 / Net I/σ(I): 8.9
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.705 / Num. unique all: 992 / CC1/2: 0.018 / % possible all: 36.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Aimless7.0.021data scaling
Coot0.8.6model building
PHENIX1.9-1692refinement
PHASERPhenix 1.9-1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B4L

4b4l


Resolution: 2.3→39.943 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.58
RfactorNum. reflection% reflection
Rfree0.267 719 4.74 %
Rwork0.2006 --
obs0.2036 15161 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 0 54 2476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092474
X-RAY DIFFRACTIONf_angle_d1.1943336
X-RAY DIFFRACTIONf_dihedral_angle_d14.712942
X-RAY DIFFRACTIONf_chiral_restr0.045368
X-RAY DIFFRACTIONf_plane_restr0.005431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.47770.33551400.26422850X-RAY DIFFRACTION99
2.4777-2.7270.31751560.24012848X-RAY DIFFRACTION99
2.727-3.12150.28541480.21312863X-RAY DIFFRACTION99
3.1215-3.93220.26321350.18642890X-RAY DIFFRACTION98
3.9322-39.94910.23171400.18492991X-RAY DIFFRACTION97

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