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- PDB-8p5j: Kinase domain of mutant human ULK1 in complex with compound WZ4003 -

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Basic information

Entry
Database: PDB / ID: 8p5j
TitleKinase domain of mutant human ULK1 in complex with compound WZ4003
ComponentsSerine/threonine-protein kinase ULK1
KeywordsTRANSFERASE / Autophagy / Unc-like 1 kinase
Function / homology
Function and homology information


neuron projection regeneration / omegasome membrane / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of autophagosome assembly / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / phagophore assembly site ...neuron projection regeneration / omegasome membrane / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of autophagosome assembly / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / phagophore assembly site / axon extension / TBC/RABGAPs / reticulophagy / Receptor Mediated Mitophagy / response to starvation / Macroautophagy / cellular response to stress / autophagosome membrane / autophagosome assembly / regulation of macroautophagy / cellular response to nutrient levels / negative regulation of protein-containing complex assembly / mitophagy / positive regulation of autophagy / autophagosome / macroautophagy / Regulation of TNFR1 signaling / recycling endosome / peptidyl-serine phosphorylation / autophagy / small GTPase binding / neuron projection development / intracellular protein localization / protein autophosphorylation / GTPase binding / mitochondrial outer membrane / protein phosphorylation / non-specific serine/threonine protein kinase / regulation of autophagy / axon / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex binding / signal transduction / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase, Ulk1/Ulk2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Serine/threonine-protein kinase, Ulk1/Ulk2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like / 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
Similarity search - Domain/homology
: / Serine/threonine-protein kinase ULK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.164 Å
AuthorsBattista, T. / Semrau, M.S. / Heroux, A. / Lolli, G. / Storici, P.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Crystal structures of ULK1 in complex with KCGS compounds
Authors: Battista, T. / Semrau, M.S. / Lolli, G. / Storici, P.
History
DepositionMay 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase ULK1
B: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3087
Polymers64,2422
Non-polymers1,0665
Water4,900272
1
A: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6423
Polymers32,1211
Non-polymers5212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6654
Polymers32,1211
Non-polymers5443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.090, 96.090, 108.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 8 - 279 / Label seq-ID: 9 - 280

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Serine/threonine-protein kinase ULK1 / Autophagy-related protein 1 homolog / ATG1 / hATG1 / Unc-51-like kinase 1


Mass: 32121.098 Da / Num. of mol.: 2 / Mutation: R245A, E245A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULK1, KIAA0722 / Production host: Escherichia coli (E. coli)
References: UniProt: O75385, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-WYT / ~{N}-[3-[5-chloranyl-2-[[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino]pyrimidin-4-yl]oxyphenyl]propanamide


Mass: 496.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H29ClN6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.3-0.8 M NaAcetate pH 6, 20-26% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.164→63.281 Å / Num. obs: 47753 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.999 / Net I/σ(I): 19.4
Reflection shellResolution: 2.164→2.201 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2362 / CC1/2: 0.697 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.164→63.281 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.253 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.141
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2001 2331 4.881 %
Rwork0.1676 45422 -
all0.169 --
obs-47753 99.937 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.156 Å2
Baniso -1Baniso -2Baniso -3
1-0.393 Å20 Å20 Å2
2---0.029 Å20 Å2
3----0.364 Å2
Refinement stepCycle: LAST / Resolution: 2.164→63.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 0 73 272 4642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124518
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164395
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.6566105
X-RAY DIFFRACTIONr_angle_other_deg0.5021.5810117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2675549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.021536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8310824
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.79910202
X-RAY DIFFRACTIONr_chiral_restr0.0770.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021044
X-RAY DIFFRACTIONr_nbd_refined0.2210.2822
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23913
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22236
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2213
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0530.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.211
X-RAY DIFFRACTIONr_nbd_other0.1860.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0880.29
X-RAY DIFFRACTIONr_mcbond_it3.9974.4732162
X-RAY DIFFRACTIONr_mcbond_other3.9874.4732162
X-RAY DIFFRACTIONr_mcangle_it5.2958.0122700
X-RAY DIFFRACTIONr_mcangle_other5.2948.0132701
X-RAY DIFFRACTIONr_scbond_it5.6685.1132356
X-RAY DIFFRACTIONr_scbond_other5.6685.1132357
X-RAY DIFFRACTIONr_scangle_it8.4399.0923396
X-RAY DIFFRACTIONr_scangle_other8.4389.0923397
X-RAY DIFFRACTIONr_lrange_it9.76343.2685004
X-RAY DIFFRACTIONr_lrange_other9.7642.954953
X-RAY DIFFRACTIONr_ncsr_local_group_10.0960.058556
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.096130.05008
12AX-RAY DIFFRACTIONLocal ncs0.096130.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.164-2.220.2721550.2513330X-RAY DIFFRACTION99.914
2.22-2.2810.2671590.2283235X-RAY DIFFRACTION99.8823
2.281-2.3470.2541530.2083139X-RAY DIFFRACTION99.9696
2.347-2.4190.2341890.1993021X-RAY DIFFRACTION100
2.419-2.4980.251410.1932965X-RAY DIFFRACTION100
2.498-2.5860.2361300.1912895X-RAY DIFFRACTION100
2.586-2.6830.2551490.1852759X-RAY DIFFRACTION100
2.683-2.7930.2221410.1812673X-RAY DIFFRACTION100
2.793-2.9170.2211260.1722583X-RAY DIFFRACTION100
2.917-3.0590.1861410.1652426X-RAY DIFFRACTION100
3.059-3.2240.2181410.1692340X-RAY DIFFRACTION99.9597
3.224-3.4190.2021070.1712213X-RAY DIFFRACTION100
3.419-3.6540.211010.1722122X-RAY DIFFRACTION100
3.654-3.9450.1871040.1591940X-RAY DIFFRACTION99.9511
3.945-4.320.1741100.1451793X-RAY DIFFRACTION99.9475
4.32-4.8280.161700.1281663X-RAY DIFFRACTION99.9423
4.828-5.5690.173780.1411472X-RAY DIFFRACTION100
5.569-6.8070.198540.1791262X-RAY DIFFRACTION100
6.807-9.5720.144540.144990X-RAY DIFFRACTION99.6183
9.572-63.2810.201280.182601X-RAY DIFFRACTION98.2812

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