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Yorodumi- EMDB-40735: Structure of human ULK1 complex core (2:2:2 stoichiometry) of the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40735 | |||||||||
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Title | Structure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Autophagy / Protein kinase / Complex / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information omegasome membrane / neuron projection regeneration / regulation of protein lipidation / ribophagy / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / autophagy of peroxisome / glycophagy / response to mitochondrial depolarisation / positive regulation of autophagosome assembly ...omegasome membrane / neuron projection regeneration / regulation of protein lipidation / ribophagy / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / autophagy of peroxisome / glycophagy / response to mitochondrial depolarisation / positive regulation of autophagosome assembly / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / protein kinase regulator activity / axon extension / TBC/RABGAPs / phagophore assembly site / autophagy of mitochondrion / reticulophagy / positive regulation of protein targeting to mitochondrion / Receptor Mediated Mitophagy / Macroautophagy / response to starvation / autophagosome membrane / positive regulation of cell size / autophagosome assembly / mitophagy / regulation of macroautophagy / negative regulation of protein-containing complex assembly / cellular response to nutrient levels / positive regulation of autophagy / protein-membrane adaptor activity / extrinsic apoptotic signaling pathway / autophagosome / protein serine/threonine kinase activator activity / liver development / negative regulation of extrinsic apoptotic signaling pathway / peptidyl-threonine phosphorylation / macroautophagy / Regulation of TNFR1 signaling / positive regulation of JNK cascade / recycling endosome / small GTPase binding / autophagy / neuron projection development / protein localization / GTPase binding / heart development / peptidyl-serine phosphorylation / nuclear membrane / mitochondrial outer membrane / protein autophosphorylation / molecular adaptor activity / lysosome / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / protein phosphorylation / negative regulation of cell population proliferation / axon / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.46 Å | |||||||||
Authors | Chen M / Hurley JH | |||||||||
Funding support | United States, 2 items
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Citation | Journal: bioRxiv Title: Structure and activation of the human autophagy-initiating ULK1C:PI3KC3-C1 supercomplex Authors: Chen M / Ren X / Cook A / Hurley JH | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40735.map.gz | 167.9 MB | EMDB map data format | |
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Header (meta data) | emd-40735-v30.xml emd-40735.xml | 20 KB 20 KB | Display Display | EMDB header |
Images | emd_40735.png | 54.9 KB | ||
Filedesc metadata | emd-40735.cif.gz | 6.6 KB | ||
Others | emd_40735_half_map_1.map.gz emd_40735_half_map_2.map.gz | 165 MB 165 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40735 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40735 | HTTPS FTP |
-Validation report
Summary document | emd_40735_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_40735_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_40735_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | emd_40735_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40735 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40735 | HTTPS FTP |
-Related structure data
Related structure data | 8srmMC 8soiC 8sorC 8sqzC 9c82C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40735.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.115 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map B
File | emd_40735_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_40735_half_map_2.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human autophagy initiation ULK1 complex core
Entire | Name: Human autophagy initiation ULK1 complex core |
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Components |
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-Supramolecule #1: Human autophagy initiation ULK1 complex core
Supramolecule | Name: Human autophagy initiation ULK1 complex core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 210 KDa |
-Macromolecule #1: RB1-inducible coiled-coil protein 1
Macromolecule | Name: RB1-inducible coiled-coil protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 73.325633 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Serine/threonine-protein kinase ULK1
Macromolecule | Name: 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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.190145 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: Autophagy-related protein 13
Macromolecule | Name: Autophagy-related protein 13 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.150997 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: KPAFSKDDIL PMDLGTFYRE FQNPPQLSSL SIDIGAQSMA EDLDSLPEKL AVHEKNVREF DAFVETLQGS DEA UniProtKB: Autophagy-related protein 13 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.35 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: 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 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2286 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL |
Output model | PDB-8srm: |