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- PDB-8soi: Structure of human ULK1 complex core (2:1:1 stoichiometry) -

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Basic information

Entry
Database: PDB / ID: 8soi
TitleStructure of human ULK1 complex core (2:1:1 stoichiometry)
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


neuron projection regeneration / omegasome membrane / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / ribophagy / response to mitochondrial depolarisation / glycophagy / positive regulation of autophagosome assembly / protein localization to phagophore assembly site / phagophore assembly site membrane ...neuron projection regeneration / omegasome membrane / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / ribophagy / response to mitochondrial depolarisation / glycophagy / positive regulation of autophagosome assembly / protein localization to phagophore assembly site / phagophore assembly site membrane / pexophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / phagophore assembly site / protein kinase regulator activity / axon extension / TBC/RABGAPs / reticulophagy / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / response to starvation / cellular response to stress / Macroautophagy / autophagosome membrane / autophagosome assembly / positive regulation of cell size / regulation of macroautophagy / negative regulation of protein-containing complex assembly / cellular response to nutrient levels / mitophagy / extrinsic apoptotic signaling pathway / protein-membrane adaptor activity / positive regulation of autophagy / autophagosome / protein serine/threonine kinase activator activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / macroautophagy / Regulation of TNFR1 signaling / liver development / recycling endosome / peptidyl-serine phosphorylation / small GTPase binding / autophagy / neuron projection development / intracellular protein localization / heart development / protein autophosphorylation / GTPase binding / nuclear membrane / defense response to virus / molecular adaptor activity / mitochondrial outer membrane / protein phosphorylation / lysosome / non-specific serine/threonine protein kinase / regulation of autophagy / negative regulation of cell population proliferation / axon / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein kinase binding / protein-containing complex binding / signal transduction / mitochondrion / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase, Ulk1/Ulk2 / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / Autophagy-related protein 13 / 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, Ulk1/Ulk2 / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / Autophagy-related protein 13 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like / 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: 4.2 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 / Year: 2023
Title: Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex
Authors: Chen, M. / Ren, X. / Cook, A. / Hurley, J.H.
History
DepositionApr 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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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: Autophagy-related protein 13


Theoretical massNumber of molelcules
Total (without water)167,5364
Polymers167,5364
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 68808.477 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: 23113.896 Da / Num. of mol.: 1
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: 6805.392 Da / Num. of mol.: 1
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
Has protein modificationY

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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: 0.188 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293 GNTi- / Plasmid: pCAG
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
2200 mMsodium chlorideNaCl1
31 mMmagnesium chlorideMgCl21
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 5 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8468

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Processing

EM software
IDNameVersionCategory
1Topaz0.2.5aparticle selection
2SerialEMimage acquisition
4cryoSPARC3.3.1CTF correction
7ISOLDE1.5model fitting
8Coot0.9.8model fitting
10cryoSPARC3.3.1initial Euler assignment
11cryoSPARC3.3.1final Euler assignment
12cryoSPARC3.3.1classification
13cryoSPARC3.3.13D reconstruction
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2156516
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 267719 / 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_d0.00310419
ELECTRON MICROSCOPYf_angle_d0.57914041
ELECTRON MICROSCOPYf_dihedral_angle_d5.0961372
ELECTRON MICROSCOPYf_chiral_restr0.0361606
ELECTRON MICROSCOPYf_plane_restr0.0031790

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