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

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Basic information

Entry
Database: PDB / ID: 9dub
TitleCrystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound SRM-25-071
ComponentsDeath-associated protein kinase 1
KeywordsTRANSFERASE / DAPK1 / DAPK1 catalytic subunit / SRM-25-071 / 4-(pyridin-4-yl)pyridazine
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 / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / : ...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 / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / : / 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 / negative regulation of translation / postsynaptic density / 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 / negative regulation of apoptotic process / GTP binding / apoptotic process / 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: 1.5 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 SRM-25-071
Authors: Minasov, G. / Winsor, J. / Roy, S.M. / Watterson, D.M. / Shuvalova, L.
History
DepositionOct 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 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)34,5639
Polymers33,7941
Non-polymers7698
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.880, 62.653, 88.323
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: 33794.367 Da / Num. of mol.: 1 / Fragment: protein kinase domain (UNP residues 2-285)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK1, DAPK / Plasmid: pASK-IBA3 / Production host: Escherichia coli (E. coli)
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1BB7 / 4-(pyridin-4-yl)pyridazine


Mass: 157.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 1.92 Å3/Da / Density % sol: 35.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
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 SRM-25-071, 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 SRM-25-071, 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: Oct 17, 2019
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 42517 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 20.9 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.023 / Rrim(I) all: 0.056 / Rsym value: 0.051 / Χ2: 1.024 / Net I/σ(I): 29.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2095 / CC1/2: 0.644 / CC star: 0.885 / Rpim(I) all: 0.45 / Χ2: 1.002 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-30002.3.15data reduction
HKL-30002.3.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→28.62 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.703 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18297 2160 5.1 %RANDOM
Rwork0.15803 ---
obs0.15929 40217 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.997 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.39 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: 1 / Resolution: 1.5→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 43 247 2528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122495
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162388
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.6593388
X-RAY DIFFRACTIONr_angle_other_deg0.4411.5795523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8145308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.783515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.10610460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.022927
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02574
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_it1.7961.9071196
X-RAY DIFFRACTIONr_mcbond_other1.7771.9061196
X-RAY DIFFRACTIONr_mcangle_it2.7183.421516
X-RAY DIFFRACTIONr_mcangle_other2.7183.4231517
X-RAY DIFFRACTIONr_scbond_it3.322.4381299
X-RAY DIFFRACTIONr_scbond_other3.1712.3411275
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0374.0921837
X-RAY DIFFRACTIONr_long_range_B_refined7.28825.812859
X-RAY DIFFRACTIONr_long_range_B_other6.92524.092779
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 164 -
Rwork0.251 2908 -
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)
12.1152-1.30350.87012.7158-1.5932.07920.06780.0598-0.1845-0.09030.02820.28530.12910.0066-0.0960.0278-0.009-0.00810.00990.00440.0567-4.2705-2.9734-2.2876
20.67540.2957-0.48460.7073-0.34380.4805-0.01240.0431-0.00230.01330.01440.00140.0289-0.0236-0.0020.0088-0.0053-0.00350.01890.00650.0055.76587.0819-9.0067
33.2032-0.1523-0.28671.35630.12450.50010.04470.07310.14540.0145-0.03750.13590.0333-0.1412-0.00730.0054-0.00890.00380.0420.00670.03625.154411.8574-11.4524
40.5995-0.1090.14860.84260.16521.16760.03220.0411-0.0134-0.03310.0299-0.018-0.02430.0662-0.0620.00340.00010.0030.0069-0.00160.021919.205811.6372-21.5378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 49
2X-RAY DIFFRACTION2A50 - 144
3X-RAY DIFFRACTION3A145 - 172
4X-RAY DIFFRACTION4A173 - 277

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