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Yorodumi- PDB-8dh7: Cryo-EM structure of Saccharomyces cerevisiae Succinyl-CoA:acetat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dh7 | ||||||
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Title | Cryo-EM structure of Saccharomyces cerevisiae Succinyl-CoA:acetate CoA-transferase (Ach1p) | ||||||
Components | Acetyl-CoA hydrolase | ||||||
Keywords | TRANSFERASE / Ach1p / Succinyl-CoA / acetate CoA-transferase | ||||||
Function / homology | Function and homology information acetyl-CoA hydrolase / acetyl-CoA hydrolase activity / propionate metabolic process, methylcitrate cycle / acetate CoA-transferase activity / acetate metabolic process / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å | ||||||
Authors | Godoy, A.S. / Song, Y. / Cheruvara, H. / Quigley, A. / Oliva, G. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs Authors: Godoy, A.S. / Song, Y. / Cheruvara, H. / Quigley, A. / Oliva, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dh7.cif.gz | 183.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dh7.ent.gz | 148.3 KB | Display | PDB format |
PDBx/mmJSON format | 8dh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/8dh7 ftp://data.pdbj.org/pub/pdb/validation_reports/dh/8dh7 | HTTPS FTP |
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-Related structure data
Related structure data | 27431MC 8dh6C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 58791.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32316, acetyl-CoA hydrolase |
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-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 | Name: Succinyl-CoA:acetate CoA-transferase / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3100 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 0.989314222 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82557 / Symmetry type: POINT | ||||||||||||||||||||||||
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