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Yorodumi- PDB-8dit: Cryo-EM structure of a HOPS core complex containing Vps33, Vps16,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dit | ||||||||||||
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Title | Cryo-EM structure of a HOPS core complex containing Vps33, Vps16, and Vps18 | ||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / HOPS / membrane tethering / SNAREs / membrane fusion / endolysosomal trafficking | ||||||||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å | ||||||||||||
Authors | Port, S.A. / Farrell, P.D. / Jeffrey, P.D. / DiMaio, F. / Hughson, F.M. | ||||||||||||
Funding support | Germany, United States, 3items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the HOPS core complex and its implication for SNARE assembly Authors: Port, S.A. / Farrell, P.D. / Jeffrey, P.D. / DiMaio, F. / Hughson, F.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dit.cif.gz | 429.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dit.ent.gz | 342 KB | Display | PDB format |
PDBx/mmJSON format | 8dit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dit_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8dit_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8dit_validation.xml.gz | 68.4 KB | Display | |
Data in CIF | 8dit_validation.cif.gz | 104.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/8dit ftp://data.pdbj.org/pub/pdb/validation_reports/di/8dit | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 77119.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Plasmid: pQLinkH-Vps33:Vps16 / Details (production host): co-expression plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+ |
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#2: Protein | Mass: 94204.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Plasmid: pQLinkH-Vps33:Vps16 / Details (production host): co-expression plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon+ |
#3: Protein | Mass: 108527.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Plasmid: pQLinkN-Vps18 / Production host: Escherichia coli (E. coli) / Variant (production host): C43 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: PELCO Easiglow, 10 mA/ 10 s discharge/ 30 s hold / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K Details: Blotting parameters: 30 seconds waiting time, blotting force 1, blot total 1 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 2000 nm / Cs: 0.03 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5.6 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3590 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 32 / Used frames/image: 1-32 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4092244 / Details: blob picker 60-280A (circular) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154917 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 5.1 Å |