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- EMDB-40735: Structure of human ULK1 complex core (2:2:2 stoichiometry) of the... -

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Basic information

Entry
Database: EMDB / ID: EMD-40735
TitleStructure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant
Map data
Sample
  • Complex: Human autophagy initiation ULK1 complex core
    • Protein or peptide: RB1-inducible coiled-coil protein 1
    • Protein or peptide: Serine/threonine-protein kinase ULK1
    • Protein or peptide: Autophagy-related protein 13
KeywordsAutophagy / Protein kinase / Complex / IMMUNE SYSTEM
Function / homology
Function and homology information


omegasome membrane / neuron projection regeneration / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / ribophagy / glycophagy / response to mitochondrial depolarisation / positive regulation of autophagosome assembly / protein localization to phagophore assembly site / phagophore assembly site membrane ...omegasome membrane / neuron projection regeneration / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / ribophagy / glycophagy / response to mitochondrial depolarisation / positive regulation of autophagosome assembly / protein localization to phagophore assembly site / phagophore assembly site membrane / autophagy of mitochondrion / pexophagy / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / axon extension / phagophore assembly site / protein kinase regulator activity / TBC/RABGAPs / reticulophagy / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Macroautophagy / cellular response to stress / response to starvation / autophagosome membrane / autophagosome assembly / positive regulation of cell size / regulation of macroautophagy / cellular response to nutrient levels / negative regulation of protein-containing complex assembly / mitophagy / protein-membrane adaptor activity / extrinsic apoptotic signaling pathway / positive regulation of autophagy / autophagosome / protein serine/threonine kinase activator activity / liver development / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / macroautophagy / Regulation of TNFR1 signaling / recycling endosome / small GTPase binding / autophagy / neuron projection development / intracellular protein localization / peptidyl-serine phosphorylation / heart development / GTPase binding / protein autophosphorylation / molecular adaptor activity / nuclear membrane / defense response to virus / mitochondrial outer membrane / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / lysosome / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of autophagy / protein phosphorylation / axon / negative regulation of cell population proliferation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex binding / 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 / 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 ...Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / Serine/threonine-protein kinase, Ulk1/Ulk2 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.46 Å
AuthorsChen M / Hurley JH
Funding support United States, 2 items
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 JH
History
DepositionMay 5, 2023-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40735.png

Downloads & links

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Map

FileDownload / File: emd_40735.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 360 pix.
= 401.4 Å		1.12 Å/pix.
x 360 pix.
= 401.4 Å		1.12 Å/pix.
x 360 pix.
= 401.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.115 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.23714544 - 0.69030666
Average (Standard dev.)-0.00029729947 (±0.012353985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 401.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_40735_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_40735_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human autophagy initiation ULK1 complex core

EntireName: Human autophagy initiation ULK1 complex core
Components
  • Complex: Human autophagy initiation ULK1 complex core
    • Protein or peptide: RB1-inducible coiled-coil protein 1
    • Protein or peptide: Serine/threonine-protein kinase ULK1
    • Protein or peptide: Autophagy-related protein 13

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Supramolecule #1: Human autophagy initiation ULK1 complex core

SupramoleculeName: Human autophagy initiation ULK1 complex core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: RB1-inducible coiled-coil protein 1

MacromoleculeName: RB1-inducible coiled-coil protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.325633 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKLYVFLVNT GTTLTFDTEL TVQTVADLKH AIQSKYKIAI QHQVLVVNGG ECMAADRRVC TYSAGTDTNP IFLFNKEMIL CDRPPAIPK TTFSTENDME IKVEESLMMP AVFHTVASRT QLALEMYEVA KKLCSFCEGL VHDEHLQHQG WAAIMANLED C SNSYQKLL ...String:
MKLYVFLVNT GTTLTFDTEL TVQTVADLKH AIQSKYKIAI QHQVLVVNGG ECMAADRRVC TYSAGTDTNP IFLFNKEMIL CDRPPAIPK TTFSTENDME IKVEESLMMP AVFHTVASRT QLALEMYEVA KKLCSFCEGL VHDEHLQHQG WAAIMANLED C SNSYQKLL FKFESIYSNY LQSIEDIKLK LTHLGTAVSV MAKIPLLECL TRHSYRECLG RLDSLPEHED SEKAEMKRST EL VLSPDMP RTTNESLLTS FPKSVEHVSP DTADAESGKE IRESCQSTVH QQDETTIDTK DGDLPFFNVS LLDWINVQDR PND VESLVR KCFDSMSRLD PRIIRPFIAE CRQTIAKLDN QNMKAIKGLE DRLYALDQMI ASCGRLVNEQ KELAQGFLAN QKRA ENLKD ASVLPDLCLS HANQLMIMLQ NHRKLLDIKQ KCTTAKQELA NNLHVRLKWC CFVMLHADQD GEKLQALLRL VIELL ERVK IVEALSTVPQ MYCLAVVEVV RRKMFIKHYR EWAGALVKDG KRLYEAEKSK RESFGKLFRK SFLRNRLFRG LDSWPP SFC TQKPRKFDCE LPDISLKDLQ FLQSFCPSEV QPFLRVPLLC DFEPLHQHVL ALHNLVKAAQ SLDEMSQTIT DLLSEQK

UniProtKB: RB1-inducible coiled-coil protein 1

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Macromolecule #2: Serine/threonine-protein kinase ULK1

MacromoleculeName: Serine/threonine-protein kinase ULK1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.190145 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEQEHTEILR GLRFTLLFVQ HVLEIAALKG SASEAAGGPE YQLQESVVAD QISLLSREWG FAEQLVLYLK VAELLSSGLQ SAIDQIRAG KLCLSSTVKQ VVRRLNELYK ASVVSCQGLS LRLQRFFLDK QRLLDRIHSI TAERLIFSHA VQMVQSAALD E MFQHREGC ...String:
MEQEHTEILR GLRFTLLFVQ HVLEIAALKG SASEAAGGPE YQLQESVVAD QISLLSREWG FAEQLVLYLK VAELLSSGLQ SAIDQIRAG KLCLSSTVKQ VVRRLNELYK ASVVSCQGLS LRLQRFFLDK QRLLDRIHSI TAERLIFSHA VQMVQSAALD E MFQHREGC VPRYHKALLL LEGLQHMLSD QADIENVTKC KLCIERRLSA LLTGICA

UniProtKB: Serine/threonine-protein kinase ULK1

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Macromolecule #3: Autophagy-related protein 13

MacromoleculeName: Autophagy-related protein 13 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.150997 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
KPAFSKDDIL PMDLGTFYRE FQNPPQLSSL SIDIGAQSMA EDLDSLPEKL AVHEKNVREF DAFVETLQGS DEA

UniProtKB: Autophagy-related protein 13

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.35 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
1.0 mMMgCl2magnesium chloride
1.0 mMC9H15O6PTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2286 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 968884
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 148675
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 148675

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8srm:
Structure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant

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