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Yorodumi- EMDB-41053: Local refinement map (2/3) of the human ULK1 complex core (EMD-40658) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41053 | |||||||||
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Title | Local refinement map (2/3) of the human ULK1 complex core (EMD-40658) | |||||||||
Map data | The local refinement map of the entry EMD-40658 (2/3) | |||||||||
Sample |
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Keywords | Autophagy / Protein kinase / Complex / IMMUNE SYSTEM | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.35 Å | |||||||||
Authors | Chen M / Hurley JH | |||||||||
Funding support | United States, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41053.map.gz | 166.1 MB | EMDB map data format | |
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Header (meta data) | emd-41053-v30.xml emd-41053.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_41053.png | 37.5 KB | ||
Others | emd_41053_half_map_1.map.gz emd_41053_half_map_2.map.gz | 165 MB 164.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41053 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41053 | HTTPS FTP |
-Validation report
Summary document | emd_41053_validation.pdf.gz | 926.1 KB | Display | EMDB validaton report |
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Full document | emd_41053_full_validation.pdf.gz | 925.7 KB | Display | |
Data in XML | emd_41053_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | emd_41053_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41053 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41053 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41053.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The local refinement map of the entry EMD-40658 (2/3) | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: The according half map (1/2)
File | emd_41053_half_map_1.map | ||||||||||||
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Annotation | The according half map (1/2) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: The according half map (2/2)
File | emd_41053_half_map_2.map | ||||||||||||
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Annotation | The according half map (2/2) | ||||||||||||
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: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 188 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: 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 / Details: 5 mA | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8468 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 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: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / 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 |