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- PDB-9miu: Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with... -

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Basic information

Entry
Database: PDB / ID: 9miu
TitleCrystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-9-039SRM.
ComponentsDeath-associated protein kinase 1
KeywordsTRANSFERASE / DAPK1 / DAPK1 catalytic subunit / MW01-9-039SRM / 6-chloro-N / N-dimethyl-5-(pyridin-4-yl)pyridazin-3-amine
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 / regulation of NMDA receptor activity / calcium/calmodulin-dependent protein kinase activity / syntaxin-1 binding / extrinsic apoptotic signaling pathway via death domain receptors ...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 / regulation of NMDA receptor activity / calcium/calmodulin-dependent protein kinase activity / syntaxin-1 binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / protein autophosphorylation / regulation of apoptotic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / calmodulin binding / postsynaptic density / regulation of autophagy / negative regulation of translation / intracellular signal transduction / protein phosphorylation / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / GTP binding / glutamatergic synapse / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / 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 / 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
Similarity search - Domain/homology
: / Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMinasov, G. / Winsor, J. / Roy, S.M. / Watterson, D.M. / Shuvalova, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)AG066722 United States
CitationJournal: To Be Published
Title: Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-9-039SRM.
Authors: Minasov, G. / Winsor, J. / Roy, S.M. / Watterson, D.M. / Shuvalova, L.
History
DepositionDec 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Death-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6146
Polymers34,9951
Non-polymers6195
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.986, 62.627, 88.501
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 / DAP kinase 1


Mass: 34994.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK1, DAPK / Plasmid: pASK-IBA3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1BLJ / 6-chloro-N,N-dimethyl-5-(pyridin-4-yl)pyridazin-3-amine


Mass: 234.685 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11ClN4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Protein: 6.6 mg/ml, 0.25M Sodium chloride, 0.1M Tris-HCl (pH 8.0); Screen: 1.8M Ammomium sulfate, 0.2M Ammonium chloride; Soak: 24h, 1mM MW01-9-039SRM, 10% DMSO, 1.8M Ammonium sulfate, 0.2M ...Details: Protein: 6.6 mg/ml, 0.25M Sodium chloride, 0.1M Tris-HCl (pH 8.0); Screen: 1.8M Ammomium sulfate, 0.2M Ammonium chloride; Soak: 24h, 1mM MW01-9-039SRM, 10% DMSO, 1.8M Ammonium sulfate, 0.2M Ammonium chloride; Cryo: 1.8M Ammonium sulfate, 25% sucrose.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2020
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 21300 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.049 / Rsym value: 0.122 / Χ2: 1.022 / Net I/σ(I): 18.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1026 / CC1/2: 0.661 / CC star: 0.892 / Rpim(I) all: 0.551 / Χ2: 0.993 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.52 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.149 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19671 1046 4.9 %RANDOM
Rwork0.15735 ---
obs0.15918 20177 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.311 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å20 Å2
2---0.12 Å2-0 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 36 142 2416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122470
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162365
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.853356
X-RAY DIFFRACTIONr_angle_other_deg0.5211.7755471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3865306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.031513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.86810452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.022891
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02558
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4542.1691191
X-RAY DIFFRACTIONr_mcbond_other2.452.1691191
X-RAY DIFFRACTIONr_mcangle_it3.5853.881508
X-RAY DIFFRACTIONr_mcangle_other3.5853.8841509
X-RAY DIFFRACTIONr_scbond_it4.3442.8371279
X-RAY DIFFRACTIONr_scbond_other4.1312.7641264
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5344.81825
X-RAY DIFFRACTIONr_long_range_B_refined8.8427.472762
X-RAY DIFFRACTIONr_long_range_B_other8.56626.832733
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 74 -
Rwork0.227 1471 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1148-2.33051.30773.2843-2.09942.99110.14260.0726-0.2345-0.16110.01450.38180.15130.0089-0.15710.032-0.0118-0.00970.0140.00020.0654-4.274-2.926-2.31
20.95890.3938-0.690.732-0.24370.5085-0.01160.07320.00790.04190.02170.02730.0106-0.0738-0.01010.0194-0.0046-0.00440.05960.00610.01965.6548.3-9.568
30.8814-0.16930.04481.18720.08481.40810.01840.0714-0.0268-0.05110.0418-0.0223-0.02760.0752-0.06020.0070.00030.00070.0160.00190.027519.2411.629-21.617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 49
2X-RAY DIFFRACTION2A50 - 172
3X-RAY DIFFRACTION3A173 - 277

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