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Yorodumi- EMDB-25989: Rhodobacter sphaeroides Mitochondrial respiratory chain complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25989 | |||||||||
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Title | Rhodobacter sphaeroides Mitochondrial respiratory chain complex | |||||||||
Map data | rsbc1 pq4 C2 classes 2 3 | |||||||||
Sample |
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Function / homology | Function and homology information respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / : / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / heme binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Cereibacter sphaeroides (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.91 Å | |||||||||
Authors | Xia D / Zhou F / Esser L / Huang R | |||||||||
Funding support | United States, 1 items
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Citation | Journal: to be published Title: Conformation Switch of Rieske ISP subunit is revealed by the Crystal Structure of Bacterial Cytochrome bc1 in Complex with Azoxystrobin Authors: Xia D / Esser L / Zhou F | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25989.map.gz | 200.4 MB | EMDB map data format | |
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Header (meta data) | emd-25989-v30.xml emd-25989.xml | 20.5 KB 20.5 KB | Display Display | EMDB header |
Images | emd_25989.png | 133.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25989 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25989 | HTTPS FTP |
-Validation report
Summary document | emd_25989_validation.pdf.gz | 430.1 KB | Display | EMDB validaton report |
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Full document | emd_25989_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | emd_25989_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | emd_25989_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25989 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25989 | HTTPS FTP |
-Related structure data
Related structure data | 7tljMC 7tayC 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_25989.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | rsbc1 pq4 C2 classes 2 3 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Cytochrome bc1 complex of rhodobacter sphaeroides inhibited by py...
+Supramolecule #1: Cytochrome bc1 complex of rhodobacter sphaeroides inhibited by py...
+Macromolecule #1: Cytochrome b
+Macromolecule #2: Cytochrome c1
+Macromolecule #3: Ubiquinol-cytochrome c reductase iron-sulfur subunit
+Macromolecule #4: 14 kDa peptide of ubiquinol-cytochrome c2 oxidoreductase complex
+Macromolecule #5: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #6: (5S)-3-anilino-5-methyl-5-(6-phenoxypyridin-3-yl)-1,3-oxazolidine...
+Macromolecule #7: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANO...
+Macromolecule #8: HEME C
+Macromolecule #9: 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 | 8 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / 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: 3 ul of sample blot for 3 sec. blot force 20. glow discharge for 60 sec with easy glow. | |||||||||||||||
Details | Cytochrome bc1 complex from Rhodobacter sphaeroides with inhibitor pyramoxadone (PQ4), frozen stock 84 mg/ml. dilute to 8 mg/ml in buffer 50mM TrisHCl, pH7.5/0.16% SMC/0.01% GDN/1mM EDTA |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.0 K / Max: 80.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 2 / Number real images: 20306 / Average exposure time: 2.5 sec. / Average electron dose: 54.5 e/Å2 / Details: 0.05s per frame for total 50 frames. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.434 µm / Calibrated defocus min: 0.836 µm / Calibrated magnification: 60241 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |