+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17461 | |||||||||
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Title | Cytochrome bc1 complex (Bos taurus) | |||||||||
Map data | Model-based sharpened map of cytochrome bc1 complex purified natively from bovine heart tissue. | |||||||||
Sample |
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Keywords | Electron Transport Chain / Complex III / Respiratory Complex / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Complex III assembly / respiratory chain complex III / Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / ubiquinone binding / Mitochondrial protein degradation / : ...Complex III assembly / respiratory chain complex III / Respiratory electron transport / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / ubiquinone binding / Mitochondrial protein degradation / : / respiratory electron transport chain / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Phillips BP / Barra IMCC / Meier TK / Rimle L / von Ballmoos C | |||||||||
Funding support | Switzerland, United Kingdom, 2 items
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Citation | Journal: To Be Published Title: Cytochrome bc1 complex (Bos taurus) Authors: Phillips BP / Barra IMCC / Meier TK / Rimle L / von Ballmoos C | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17461.map.gz | 80 MB | EMDB map data format | |
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Header (meta data) | emd-17461-v30.xml emd-17461.xml | 30.5 KB 30.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17461_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_17461.png | 87.4 KB | ||
Filedesc metadata | emd-17461.cif.gz | 8.1 KB | ||
Others | emd_17461_half_map_1.map.gz emd_17461_half_map_2.map.gz | 95.4 MB 95.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17461 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17461 | HTTPS FTP |
-Validation report
Summary document | emd_17461_validation.pdf.gz | 755.6 KB | Display | EMDB validaton report |
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Full document | emd_17461_full_validation.pdf.gz | 755.2 KB | Display | |
Data in XML | emd_17461_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | emd_17461_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17461 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17461 | HTTPS FTP |
-Related structure data
Related structure data | 8p65MC 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_17461.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Model-based sharpened map of cytochrome bc1 complex purified natively from bovine heart tissue. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.462 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A of locally filtered bovine cytochrome...
File | emd_17461_half_map_1.map | ||||||||||||
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Annotation | Half map A of locally filtered bovine cytochrome bc1 complex, produced in CryoSPARC. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of locally filtered bovine cytochrome...
File | emd_17461_half_map_2.map | ||||||||||||
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Annotation | Half map B of locally filtered bovine cytochrome bc1 complex, produced in CryoSPARC. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cytochrome bc1 complex (bos taurus)
+Supramolecule #1: Cytochrome bc1 complex (bos taurus)
+Macromolecule #1: Cytochrome b-c1 complex subunit 1, mitochondrial
+Macromolecule #2: Cytochrome b-c1 complex subunit 2, mitochondrial
+Macromolecule #3: Cytochrome b
+Macromolecule #4: Cytochrome c1, heme protein, mitochondrial
+Macromolecule #5: Cytochrome b-c1 complex subunit Rieske, mitochondrial
+Macromolecule #6: Cytochrome b-c1 complex subunit 7
+Macromolecule #7: Cytochrome b-c1 complex subunit 8
+Macromolecule #8: Cytochrome b-c1 complex subunit 6, mitochondrial
+Macromolecule #9: Cytochrome b-c1 complex subunit 9
+Macromolecule #10: Cytochrome b-c1 complex subunit 9
+Macromolecule #11: Cytochrome b-c1 complex subunit 10
+Macromolecule #12: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #13: HEME C
+Macromolecule #14: FE2/S2 (INORGANIC) CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time of 4s with blot force of -3. |
Details | Monodisperse sample was purified un-tagged from bovine heart tissue and reconstituted into peptidiscs before freezing. |
-Electron microscopy
Microscope | TFS GLACIOS |
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Temperature | Min: 80.0 K / Max: 90.5 K |
Alignment procedure | Coma free - Residual tilt: 10.0 mrad |
Specialist optics | Phase plate: OTHER / Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV / Details: Tuned using TFS Sherpa Software |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number real images: 3947 / Average exposure time: 8.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.75 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 85000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.75 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 85000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |