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- PDB-6hyo: Structure of ULK1 LIR motif bound to GABARAP -

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Basic information

Entry
Database: PDB / ID: 6hyo
TitleStructure of ULK1 LIR motif bound to GABARAP
ComponentsSerine/threonine-protein kinase ULK1,Gamma-aminobutyric acid receptor-associated protein
KeywordsSIGNALING PROTEIN / Autophagy / ATG8 / LIR
Function / homology
Function and homology information


neuron projection regeneration / omegasome membrane / negative regulation of collateral sprouting / positive regulation of protein K48-linked ubiquitination / Atg1/ULK1 kinase complex / regulation of Rac protein signal transduction / positive regulation of autophagosome assembly / phagophore assembly site membrane / GABA receptor binding / piecemeal microautophagy of the nucleus ...neuron projection regeneration / omegasome membrane / negative regulation of collateral sprouting / positive regulation of protein K48-linked ubiquitination / Atg1/ULK1 kinase complex / regulation of Rac protein signal transduction / positive regulation of autophagosome assembly / phagophore assembly site membrane / GABA receptor binding / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / phosphatidylethanolamine binding / regulation of tumor necrosis factor-mediated signaling pathway / phagophore assembly site / axon extension / TBC/RABGAPs / cellular response to nitrogen starvation / reticulophagy / microtubule associated complex / Receptor Mediated Mitophagy / response to starvation / cellular response to stress / Macroautophagy / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum / autophagosome membrane / axoneme / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome assembly / autophagosome maturation / regulation of macroautophagy / protein targeting / negative regulation of protein-containing complex assembly / beta-tubulin binding / cellular response to nutrient levels / mitophagy / sperm midpiece / positive regulation of autophagy / autophagosome / macroautophagy / Regulation of TNFR1 signaling / recycling endosome / peptidyl-serine phosphorylation / GABA-ergic synapse / small GTPase binding / autophagy / microtubule cytoskeleton organization / neuron projection development / intracellular protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / protein autophosphorylation / GTPase binding / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / mitochondrial outer membrane / protein phosphorylation / lysosome / non-specific serine/threonine protein kinase / regulation of autophagy / Golgi membrane / negative regulation of cell population proliferation / axon / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / signal transduction / ATP binding / identical protein binding / plasma membrane / 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 / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) ...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 / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Serine/threonine-protein kinase ULK1 / Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsMouilleron, S. / Wirth, M. / Zhang, W. / O'Reilly, N. / Tooze, S. / Johansen, T. / Razi, M. / Nyoni, L. / Joshi, D.
CitationJournal: Nat Commun / Year: 2019
Title: Molecular determinants regulating selective binding of autophagy adapters and receptors to ATG8 proteins.
Authors: Wirth, M. / Zhang, W. / Razi, M. / Nyoni, L. / Joshi, D. / O'Reilly, N. / Johansen, T. / Tooze, S.A. / Mouilleron, S.
History
DepositionOct 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase ULK1,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7269
Polymers15,9351
Non-polymers7918
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint20 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.720, 100.720, 100.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-471-

HOH

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Components

#1: Protein Serine/threonine-protein kinase ULK1,Gamma-aminobutyric acid receptor-associated protein / Autophagy-related protein 1 homolog / hATG1 / Unc-51-like kinase 1 / GABA(A) receptor-associated ...Autophagy-related protein 1 homolog / hATG1 / Unc-51-like kinase 1 / GABA(A) receptor-associated protein / MM46


Mass: 15935.272 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULK1, KIAA0722, GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli)
References: UniProt: O75385, UniProt: O95166, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M MgCl2. 0.1 M Na cacodylate pH 6.5, 20% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.07→41.12 Å / Num. obs: 74520 / % possible obs: 99.9 % / Redundancy: 18.6 % / Biso Wilson estimate: 14 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.01 / Rrim(I) all: 0.05 / Net I/σ(I): 23.9
Reflection shellResolution: 1.07→1.1 Å / Redundancy: 14.6 % / Rmerge(I) obs: 1.65 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7428 / CC1/2: 0.62 / Rpim(I) all: 0.44 / Rrim(I) all: 1.71 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNU

1gnu


Resolution: 1.07→41.119 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.31
RfactorNum. reflection% reflection
Rfree0.1608 3593 4.82 %
Rwork0.1416 --
obs0.1425 74519 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.07→41.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 52 171 1299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131284
X-RAY DIFFRACTIONf_angle_d1.3921738
X-RAY DIFFRACTIONf_dihedral_angle_d23.778524
X-RAY DIFFRACTIONf_chiral_restr0.111177
X-RAY DIFFRACTIONf_plane_restr0.011227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0703-1.08440.24121790.24862694X-RAY DIFFRACTION100
1.0844-1.09920.26281250.22732722X-RAY DIFFRACTION100
1.0992-1.11490.20691450.21012704X-RAY DIFFRACTION100
1.1149-1.13160.20751320.18012712X-RAY DIFFRACTION100
1.1316-1.14920.16581070.16572765X-RAY DIFFRACTION100
1.1492-1.16810.20561370.1552673X-RAY DIFFRACTION100
1.1681-1.18820.15891330.1452700X-RAY DIFFRACTION100
1.1882-1.20980.14941460.13772694X-RAY DIFFRACTION100
1.2098-1.23310.15161490.12722710X-RAY DIFFRACTION100
1.2331-1.25830.16161230.13522748X-RAY DIFFRACTION100
1.2583-1.28560.15781410.12452705X-RAY DIFFRACTION100
1.2856-1.31560.16211190.11832735X-RAY DIFFRACTION100
1.3156-1.34850.13881680.11432672X-RAY DIFFRACTION100
1.3485-1.38490.12671160.11072748X-RAY DIFFRACTION100
1.3849-1.42570.13351590.1072703X-RAY DIFFRACTION100
1.4257-1.47170.15231260.10562710X-RAY DIFFRACTION100
1.4717-1.52430.1181370.10762718X-RAY DIFFRACTION100
1.5243-1.58530.12881400.10562742X-RAY DIFFRACTION100
1.5853-1.65750.13191360.10892721X-RAY DIFFRACTION100
1.6575-1.74490.13581650.11622702X-RAY DIFFRACTION100
1.7449-1.85420.13881350.1222751X-RAY DIFFRACTION100
1.8542-1.99730.14251200.12882746X-RAY DIFFRACTION100
1.9973-2.19830.15461520.13032740X-RAY DIFFRACTION100
2.1983-2.51640.16231420.14922743X-RAY DIFFRACTION100
2.5164-3.17020.18231230.16242809X-RAY DIFFRACTION100
3.1702-41.14910.17751380.15762859X-RAY DIFFRACTION100

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