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- PDB-8p5g: Kinase domain of wild type human ULK1 in complex with compound CC... -

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Basic information

Entry
Database: PDB / ID: 8p5g
TitleKinase domain of wild type human ULK1 in complex with compound CCT241533
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 / cellular response to stress / Macroautophagy / autophagosome membrane / autophagosome assembly / regulation of macroautophagy / negative regulation of protein-containing complex assembly / cellular response to nutrient levels / mitophagy / positive regulation of autophagy / autophagosome / macroautophagy / Regulation of TNFR1 signaling / recycling endosome / peptidyl-serine phosphorylation / small GTPase binding / autophagy / neuron projection development / intracellular protein localization / protein autophosphorylation / GTPase binding / mitochondrial outer membrane / protein phosphorylation / non-specific serine/threonine protein kinase / regulation of autophagy / negative regulation of cell population proliferation / axon / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex binding / signal transduction / ATP binding / identical protein binding / cytoplasm / cytosol
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
Chem-XBJ / Serine/threonine-protein kinase ULK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.019 Å
AuthorsBattista, T. / Semrau, M.S. / Heroux, A. / Lolli, G. / Storici, P.
Funding support Italy, 1items
OrganizationGrant numberCountry
Other government Italy
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 13, 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)65,55910
Polymers64,5302
Non-polymers1,0288
Water5,242291
1
A: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7795
Polymers32,2651
Non-polymers5144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7795
Polymers32,2651
Non-polymers5144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.800, 111.670, 84.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
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: 32265.246 Da / Num. of mol.: 2
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-XBJ / 4-FLUORO-2-(4-{[(3S,4R)-4-(1-HYDROXY-1-METHYLETHYL)PYRROLIDIN-3-YL]AMINO}-6,7-DIMETHOXYQUINAZOLIN-2-YL)PHENOL


Mass: 442.483 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27FN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 3.62 Å3/Da / Density % sol: 65.98 %
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: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.019→67.383 Å / Num. obs: 60175 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.999 / Net I/σ(I): 16.9
Reflection shellResolution: 2.019→2.054 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2959 / CC1/2: 0.789 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
pointless1.12.12data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.019→67.383 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.795 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2269 3109 5.167 %
Rwork0.1839 57066 -
all0.186 --
obs-60175 99.927 %
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: 45.019 Å2
Baniso -1Baniso -2Baniso -3
1-2.644 Å20 Å2-0 Å2
2---1.843 Å20 Å2
3----0.801 Å2
Refinement stepCycle: LAST / Resolution: 2.019→67.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 70 291 4645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124556
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164447
X-RAY DIFFRACTIONr_angle_refined_deg1.471.6516182
X-RAY DIFFRACTIONr_angle_other_deg0.4981.57710252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.035567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.614534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45310845
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.07810206
X-RAY DIFFRACTIONr_chiral_restr0.0730.2689
X-RAY DIFFRACTIONr_chiral_restr_other0.0190.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021045
X-RAY DIFFRACTIONr_nbd_refined0.2180.2925
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.24185
X-RAY DIFFRACTIONr_nbtor_refined0.1880.22227
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22477
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.150.213
X-RAY DIFFRACTIONr_nbd_other0.220.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.218
X-RAY DIFFRACTIONr_mcbond_it3.964.3862168
X-RAY DIFFRACTIONr_mcbond_other3.9484.3862168
X-RAY DIFFRACTIONr_mcangle_it4.987.8452713
X-RAY DIFFRACTIONr_mcangle_other4.9797.8462714
X-RAY DIFFRACTIONr_scbond_it5.434.9892388
X-RAY DIFFRACTIONr_scbond_other5.4294.992389
X-RAY DIFFRACTIONr_scangle_it7.9088.8923449
X-RAY DIFFRACTIONr_scangle_other7.9078.8923450
X-RAY DIFFRACTIONr_lrange_it9.23242.8415255
X-RAY DIFFRACTIONr_lrange_other9.23542.1455192
X-RAY DIFFRACTIONr_ncsr_local_group_10.1020.058772
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.102220.05008
12AX-RAY DIFFRACTIONLocal ncs0.102220.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.019-2.0710.3052340.274165X-RAY DIFFRACTION99.7054
2.071-2.1280.2881870.2444083X-RAY DIFFRACTION100
2.128-2.190.2792280.2233924X-RAY DIFFRACTION99.9519
2.19-2.2570.2952070.2213845X-RAY DIFFRACTION100
2.257-2.3310.2442020.2043745X-RAY DIFFRACTION99.9747
2.331-2.4130.2391880.2023609X-RAY DIFFRACTION99.9211
2.413-2.5040.2732000.1963457X-RAY DIFFRACTION99.918
2.504-2.6060.2921730.2073381X-RAY DIFFRACTION100
2.606-2.7210.2371910.1913214X-RAY DIFFRACTION99.9413
2.721-2.8540.2511740.1943078X-RAY DIFFRACTION99.8465
2.854-3.0080.2241650.1872931X-RAY DIFFRACTION99.9032
3.008-3.190.2391480.1782811X-RAY DIFFRACTION99.9662
3.19-3.410.2151600.1842608X-RAY DIFFRACTION100
3.41-3.6820.1991330.1832467X-RAY DIFFRACTION99.9616
3.682-4.0330.2021350.1762252X-RAY DIFFRACTION99.9581
4.033-4.5070.1941090.152072X-RAY DIFFRACTION100
4.507-5.20.213960.1491838X-RAY DIFFRACTION99.9483
5.2-6.3590.224930.1951573X-RAY DIFFRACTION100
6.359-8.9540.242520.1691257X-RAY DIFFRACTION100
8.954-67.3830.161340.184756X-RAY DIFFRACTION99.4962

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