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Yorodumi- EMDB-14123: Cryo-EM structure of catalytically active Spinacia oleracea cytoc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14123 | |||||||||
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Title | Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex with endogenous plastoquinones at 2.7 A resolution | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information plastoquinol--plastocyanin reductase activity / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / : / : / photosynthetic electron transport chain / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c ...plastoquinol--plastocyanin reductase activity / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / : / : / photosynthetic electron transport chain / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / chloroplast thylakoid membrane / photosynthesis / 2 iron, 2 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / iron ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Spinacia oleracea (spinach) / spinach (spinach) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Sarewicz M / Szwalec M / Indyka P / Rawski M / Pintscher S / Pietras R / Mielecki B / Jaciuk M / Glatt S / Osyczka A | |||||||||
Funding support | Poland, 2 items
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Citation | Journal: Sci Adv / Year: 2023 Title: High-resolution cryo-EM structures of plant cytochrome bf at work. Authors: Marcin Sarewicz / Mateusz Szwalec / Sebastian Pintscher / Paulina Indyka / Michał Rawski / Rafał Pietras / Bohun Mielecki / Łukasz Koziej / Marcin Jaciuk / Sebastian Glatt / Artur Osyczka / Abstract: Plants use solar energy to power cellular metabolism. The oxidation of plastoquinol and reduction of plastocyanin by cytochrome bf (Cyt bf) is known as one of the key steps of photosynthesis, but the ...Plants use solar energy to power cellular metabolism. The oxidation of plastoquinol and reduction of plastocyanin by cytochrome bf (Cyt bf) is known as one of the key steps of photosynthesis, but the catalytic mechanism in the plastoquinone oxidation site (Q) remains elusive. Here, we describe two high-resolution cryo-EM structures of the spinach Cyt bf homodimer with endogenous plastoquinones and in complex with plastocyanin. Three plastoquinones are visible and line up one after another head to tail near Q in both monomers, indicating the existence of a channel in each monomer. Therefore, quinones appear to flow through Cyt bf in one direction, transiently exposing the redox-active ring of quinone during catalysis. Our work proposes an unprecedented one-way traffic model that explains efficient quinol oxidation during photosynthesis and respiration. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14123.map.gz | 230.2 MB | EMDB map data format | |
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Header (meta data) | emd-14123-v30.xml emd-14123.xml | 25.8 KB 25.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14123_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_14123.png | 105.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14123 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14123 | HTTPS FTP |
-Validation report
Summary document | emd_14123_validation.pdf.gz | 514.2 KB | Display | EMDB validaton report |
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Full document | emd_14123_full_validation.pdf.gz | 513.8 KB | Display | |
Data in XML | emd_14123_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | emd_14123_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14123 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14123 | HTTPS FTP |
-Related structure data
Related structure data | 7qrmMC 7zyvC 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_14123.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Cytochrome b6f complex
+Supramolecule #1: Cytochrome b6f complex
+Macromolecule #1: Cytochrome b6
+Macromolecule #2: Cytochrome b6-f complex subunit 4
+Macromolecule #3: Cytochrome f
+Macromolecule #4: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic
+Macromolecule #5: Cytochrome b6-f complex subunit 6
+Macromolecule #6: Cytochrome b6-f complex subunit 7
+Macromolecule #7: Cytochrome b6-f complex subunit 5
+Macromolecule #8: Cytochrome b6-f complex subunit 8
+Macromolecule #9: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #10: HEME C
+Macromolecule #11: CHLOROPHYLL A
+Macromolecule #12: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #13: UNDECYL-MALTOSIDE
+Macromolecule #14: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #15: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #16: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #17: BETA-CAROTENE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.3 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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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: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 7784 / Average exposure time: 1.82 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7qrm: |