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- PDB-8srm: Structure of human ULK1 complex core (2:2:2 stoichiometry) of the... -

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Basic information

Entry
Database: PDB / ID: 8srm
TitleStructure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant
Components
  • Autophagy-related protein 13
  • RB1-inducible coiled-coil protein 1
  • Serine/threonine-protein kinase ULK1
KeywordsIMMUNE SYSTEM / Autophagy / Protein kinase / Complex
Function / homology
Function and homology information


omegasome membrane / regulation of protein lipidation / glycophagy / neuron projection regeneration / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / positive regulation of autophagosome assembly / nucleophagy / protein localization to phagophore assembly site ...omegasome membrane / regulation of protein lipidation / glycophagy / neuron projection regeneration / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / positive regulation of autophagosome assembly / nucleophagy / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / axon extension / phagophore assembly site / reticulophagy / TBC/RABGAPs / positive regulation of protein targeting to mitochondrion / Macroautophagy / Receptor Mediated Mitophagy / response to starvation / autophagosome membrane / cellular response to nutrient levels / mitophagy / autophagosome assembly / positive regulation of cell size / autophagosome / regulation of macroautophagy / negative regulation of protein-containing complex assembly / positive regulation of autophagy / protein-membrane adaptor activity / extrinsic apoptotic signaling pathway / protein serine/threonine kinase activator activity / liver development / negative regulation of extrinsic apoptotic signaling pathway / macroautophagy / Regulation of TNFR1 signaling / positive regulation of JNK cascade / peptidyl-threonine phosphorylation / protein localization / recycling endosome / small GTPase binding / autophagy / neuron projection development / GTPase binding / heart development / peptidyl-serine phosphorylation / nuclear membrane / mitochondrial outer membrane / protein autophosphorylation / lysosome / molecular adaptor activity / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / cell cycle / axon / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / signal transduction / mitochondrion / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / Serine/threonine-protein kinase, Ulk1/Ulk2 / : / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / Serine/threonine-protein kinase Atg1-like / Autophagy-related protein 13, N-terminal ...Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / Serine/threonine-protein kinase, Ulk1/Ulk2 / : / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / Serine/threonine-protein kinase Atg1-like / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / HORMA 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
Similarity search - Domain/homology
Autophagy-related protein 13 / Serine/threonine-protein kinase ULK1 / RB1-inducible coiled-coil protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.46 Å
AuthorsChen, M. / Hurley, J.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111730 United States
Michael J. Fox FoundationASAP-000350 United States
CitationJournal: bioRxiv
Title: Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex
Authors: Chen, M. / Ren, X. / Cook, A. / Hurley, J.H.
History
DepositionMay 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RB1-inducible coiled-coil protein 1
B: RB1-inducible coiled-coil protein 1
C: Serine/threonine-protein kinase ULK1
D: Serine/threonine-protein kinase ULK1
E: Autophagy-related protein 13
F: Autophagy-related protein 13


Theoretical massNumber of molelcules
Total (without water)211,3346
Polymers211,3346
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein RB1-inducible coiled-coil protein 1 / FAK family kinase-interacting protein of 200 kDa / FIP200


Mass: 73325.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RB1CC1, KIAA0203, RBICC / Production host: Homo sapiens (human) / References: UniProt: Q8TDY2
#2: Protein Serine/threonine-protein kinase ULK1 / Autophagy-related protein 1 homolog / ATG1 / hATG1 / Unc-51-like kinase 1


Mass: 24190.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULK1, KIAA0722 / Production host: Homo sapiens (human)
References: UniProt: O75385, non-specific serine/threonine protein kinase
#3: Protein Autophagy-related protein 13 /


Mass: 8150.997 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG13, KIAA0652 / Production host: Homo sapiens (human) / References: UniProt: O75143

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human autophagy initiation ULK1 complex core / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.21 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaClSodium chloride1
31 mMmagnesium chlorideMgCl21
41 mMTCEPC9H15O6P1
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 25 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 36000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2286

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Processing

EM software
IDNameVersionCategory
1Topaz0.2.5aparticle selection
4cryoSPARC3.3.1CTF correction
7ISOLDE1.5model fitting
8Coot0.9.8model fitting
10cryoSPARC3.3.1initial Euler assignment
11cryoSPARC3.3.1final Euler assignment
13cryoSPARC3.3.13D reconstruction
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 968884
3D reconstructionResolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148675 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025760
ELECTRON MICROSCOPYf_angle_d0.3498018
ELECTRON MICROSCOPYf_dihedral_angle_d4.2941150
ELECTRON MICROSCOPYf_chiral_restr0.0331121
ELECTRON MICROSCOPYf_plane_restr0.0021150

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