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- EMDB-40658: Structure of human ULK1 complex core (2:1:1 stoichiometry) -

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Basic information

Entry
Database: EMDB / ID: EMD-40658
TitleStructure of human ULK1 complex core (2:1:1 stoichiometry)
Map dataComposite map
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


neuron projection regeneration / omegasome membrane / regulation of protein lipidation / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / glycophagy / response to mitochondrial depolarisation / protein localization to phagophore assembly site / ribophagy / axon extension ...neuron projection regeneration / omegasome membrane / regulation of protein lipidation / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / glycophagy / response to mitochondrial depolarisation / protein localization to phagophore assembly site / ribophagy / axon extension / positive regulation of autophagosome assembly / phagophore assembly site membrane / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / pexophagy / protein kinase regulator activity / phagophore assembly site / regulation of tumor necrosis factor-mediated signaling pathway / TBC/RABGAPs / kinase activator activity / reticulophagy / : / cellular response to stress / response to starvation / Receptor Mediated Mitophagy / Macroautophagy / autophagosome membrane / autophagosome assembly / mitophagy / negative regulation of protein-containing complex assembly / cellular response to nutrient levels / regulation of macroautophagy / protein-membrane adaptor activity / positive regulation of autophagy / autophagosome / macroautophagy / Regulation of TNFR1 signaling / peptidyl-serine phosphorylation / regulation of autophagy / recycling endosome / intracellular protein localization / neuron projection development / small GTPase binding / autophagy / protein autophosphorylation / GTPase binding / molecular adaptor activity / protein phosphorylation / mitochondrial outer membrane / non-specific serine/threonine protein kinase / lysosome / negative regulation of cell population proliferation / protein serine kinase activity / axon / protein serine/threonine kinase activity / protein kinase binding / endoplasmic reticulum membrane / protein-containing complex binding / signal transduction / mitochondrion / DNA-templated transcription / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
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, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 ...Serine/threonine-protein kinase, Ulk1/Ulk2 / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11 / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / 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: 4.2 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 / Year: 2023
Title: Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex
Authors: Chen M / Ren X / Cook A / Hurley JH
History
DepositionApr 28, 2023-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40658.png

Downloads & links

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Map

FileDownload / File: emd_40658.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 360 pix.
= 378. Å		1.05 Å/pix.
x 360 pix.
= 378. Å		1.05 Å/pix.
x 360 pix.
= 378. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.799028 - 2.6431427
Average (Standard dev.)-0.0015839976 (±0.03156052)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 377.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Consensus map

Fileemd_40658_additional_1.map
AnnotationConsensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refinement map 2/3

Fileemd_40658_additional_2.map
AnnotationLocal refinement map 2/3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refinement map 1/3

Fileemd_40658_additional_3.map
AnnotationLocal refinement map 1/3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refinement map 3/3

Fileemd_40658_additional_4.map
AnnotationLocal refinement map 3/3
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: 188 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: 68.808477 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 QPFLRVP

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: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.113896 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HTEILRGLRF TLLFVQHVLE IAALKGSASE AAGGPEYQLQ ESVVADQISL LSREWGFAEQ LVLYLKVAEL LSSGLQSAID QIRAGKLCL SSTVKQVVRR LNELYKASVV SCQGLSLRLQ RFFLDKQRLL DRIHSITAER LIFSHAVQMV QSAALDEMFQ H REGCVPRY ...String:
HTEILRGLRF TLLFVQHVLE IAALKGSASE AAGGPEYQLQ ESVVADQISL LSREWGFAEQ LVLYLKVAEL LSSGLQSAID QIRAGKLCL SSTVKQVVRR LNELYKASVV SCQGLSLRLQ RFFLDKQRLL DRIHSITAER LIFSHAVQMV QSAALDEMFQ H REGCVPRY HKALLLLEGL QHMLSDQADI ENVTKCKLCI ERRLSAL

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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.805392 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DLGTFYREFQ NPPQLSSLSI DIGAQSMAED LDSLPEKLAV HEKNVREFDA FVETLQGSDE A

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

Concentration0.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
200.0 mMNaClsodium chloride
1.0 mMMgCl2magnesium chloride
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: GOLD / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Details: 5 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8468 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 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: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2156516
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 267719
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: 267719 / Software - Name: cryoSPARC (ver. 3.3.1)

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

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