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Yorodumi- EMDB-27431: Cryo-EM structure of Saccharomyces cerevisiae Succinyl-CoA:acetat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27431 | |||||||||
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Title | Cryo-EM structure of Saccharomyces cerevisiae Succinyl-CoA:acetate CoA-transferase (Ach1p) | |||||||||
Map data | map sharp | |||||||||
Sample |
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Keywords | Ach1p / Succinyl-CoA / acetate CoA-transferase / TRANSFERASE | |||||||||
Function / homology | Function and homology information acetyl-CoA hydrolase / acetyl-CoA hydrolase activity / acetate CoA-transferase activity / acetate metabolic process / mitochondrion / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
Authors | Godoy AS / Song Y / Cheruvara H / Quigley A / Oliva G | |||||||||
Funding support | Brazil, 1 items
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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 AS / Song Y / Cheruvara H / Quigley A / Oliva G | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27431.map.gz | 229.9 MB | EMDB map data format | |
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Header (meta data) | emd-27431-v30.xml emd-27431.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27431_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_27431.png | 83.9 KB | ||
Masks | emd_27431_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-27431.cif.gz | 5.2 KB | ||
Others | emd_27431_additional_1.map.gz emd_27431_half_map_1.map.gz emd_27431_half_map_2.map.gz | 122 MB 226.2 MB 226.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27431 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27431 | HTTPS FTP |
-Validation report
Summary document | emd_27431_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_27431_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_27431_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | emd_27431_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27431 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27431 | HTTPS FTP |
-Related structure data
Related structure data | 8dh7MC 8dh6C 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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-Map
File | Download / File: emd_27431.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | map sharp | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.831 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27431_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: map
File | emd_27431_additional_1.map | ||||||||||||
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Annotation | map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfA
File | emd_27431_half_map_1.map | ||||||||||||
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Annotation | halfA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27431_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Succinyl-CoA:acetate CoA-transferase
Entire | Name: Succinyl-CoA:acetate CoA-transferase |
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Components |
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-Supramolecule #1: Succinyl-CoA:acetate CoA-transferase
Supramolecule | Name: Succinyl-CoA:acetate CoA-transferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Acetyl-CoA hydrolase
Macromolecule | Name: Acetyl-CoA hydrolase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: acetyl-CoA hydrolase |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 58.791785 KDa |
Sequence | String: MTISNLLKQR VRYAPYLKKV KEAHELIPLF KNGQYLGWSG FTGVGTPKAV PEALIDHVEK NNLQGKLRFN LFVGASAGPE ENRWAEHDM IIKRAPHQVG KPIAKAINQG RIEFFDKHLS MFPQDLTYGF YTRERKDNKI LDYTIIEATA IKEDGSIVPG P SVGGSPEF ...String: MTISNLLKQR VRYAPYLKKV KEAHELIPLF KNGQYLGWSG FTGVGTPKAV PEALIDHVEK NNLQGKLRFN LFVGASAGPE ENRWAEHDM IIKRAPHQVG KPIAKAINQG RIEFFDKHLS MFPQDLTYGF YTRERKDNKI LDYTIIEATA IKEDGSIVPG P SVGGSPEF ITVSDKVIIE VNTATPSFEG IHDIDMPVNP PFRKPYPYLK VDDKCGVDSI PVDPEKVVAI VESTMRDQVP PN TPSDDMS RAIAGHLVEF FRNEVKHGRL PENLLPLQSG IGNIANAVIE GLAGAQFKHL TVWTEVLQDS FLDLFENGSL DYA TATSVR LTEKGFDRAF ANWENFKHRL CLRSQVVSNN PEMIRRLGVI AMNTPVEVDI YAHANSTNVN GSRMLNGLGG SADF LRNAK LSIMHAPSAR PTKVDPTGIS TIVPMASHVD QTEHDLDILV TDQGLADLRG LSPKERAREI INKCAHPDYQ ALLTD YLDR AEHYAKKHNC LHEPHMLKNA FKFHTNLAEK GTMKVDSWEP VD UniProtKB: Acetyl-CoA hydrolase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 0.989314222 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |