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Yorodumi- EMDB-4981: 3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4981 | ||||||||||||
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Title | 3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules | ||||||||||||
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Sample |
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Function / homology | Function and homology information cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / : / photosynthetic electron transport chain / mitochondrial electron transport, ubiquinol to cytochrome c / chloroplast thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity ...cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / : / photosynthetic electron transport chain / mitochondrial electron transport, ubiquinol to cytochrome c / chloroplast thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain / proton transmembrane transport / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / iron ion binding / heme binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Spinacia oleracea (spinach) / Spinach (spinach) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.58 Å | ||||||||||||
Authors | Malone LA / Qian P / Mayneord GE / Hitchcock A / Farmer D / Thompson R / Swainsbury DJK / Ranson N / Hunter CN / Johnson MP | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Nature / Year: 2019 Title: Cryo-EM structure of the spinach cytochrome bf complex at 3.6 Å resolution. Authors: Lorna A Malone / Pu Qian / Guy E Mayneord / Andrew Hitchcock / David A Farmer / Rebecca F Thompson / David J K Swainsbury / Neil A Ranson / C Neil Hunter / Matthew P Johnson / Abstract: The cytochrome b f (cytb f ) complex has a central role in oxygenic photosynthesis, linking electron transfer between photosystems I and II and converting solar energy into a transmembrane ...The cytochrome b f (cytb f ) complex has a central role in oxygenic photosynthesis, linking electron transfer between photosystems I and II and converting solar energy into a transmembrane proton gradient for ATP synthesis. Electron transfer within cytb f occurs via the quinol (Q) cycle, which catalyses the oxidation of plastoquinol (PQH) and the reduction of both plastocyanin (PC) and plastoquinone (PQ) at two separate sites via electron bifurcation. In higher plants, cytb f also acts as a redox-sensing hub, pivotal to the regulation of light harvesting and cyclic electron transfer that protect against metabolic and environmental stresses. Here we present a 3.6 Å resolution cryo-electron microscopy (cryo-EM) structure of the dimeric cytb f complex from spinach, which reveals the structural basis for operation of the Q cycle and its redox-sensing function. The complex contains up to three natively bound PQ molecules. The first, PQ1, is located in one cytb f monomer near the PQ oxidation site (Q) adjacent to haem b and chlorophyll a. Two conformations of the chlorophyll a phytyl tail were resolved, one that prevents access to the Q site and another that permits it, supporting a gating function for the chlorophyll a involved in redox sensing. PQ2 straddles the intermonomer cavity, partially obstructing the PQ reduction site (Q) on the PQ1 side and committing the electron transfer network to turnover at the occupied Q site in the neighbouring monomer. A conformational switch involving the haem c propionate promotes two-electron, two-proton reduction at the Q site and avoids formation of the reactive intermediate semiquinone. The location of a tentatively assigned third PQ molecule is consistent with a transition between the Q and Q sites in opposite monomers during the Q cycle. The spinach cytb f structure therefore provides new insights into how the complex fulfils its catalytic and regulatory roles in photosynthesis. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4981.map.gz | 106.5 MB | EMDB map data format | |
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Header (meta data) | emd-4981-v30.xml emd-4981.xml | 26.8 KB 26.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4981_fsc.xml | 11 KB | Display | FSC data file |
Images | emd_4981.png | 168.2 KB | ||
Masks | emd_4981_msk_1.map | 113.6 MB | Mask map | |
Others | emd_4981_half_map_1.map.gz emd_4981_half_map_2.map.gz | 89.4 MB 89.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4981 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4981 | HTTPS FTP |
-Validation report
Summary document | emd_4981_validation.pdf.gz | 462.2 KB | Display | EMDB validaton report |
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Full document | emd_4981_full_validation.pdf.gz | 461.4 KB | Display | |
Data in XML | emd_4981_validation.xml.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4981 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4981 | HTTPS FTP |
-Related structure data
Related structure data | 6rqfMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4981.map.gz / Format: CCP4 / Size: 113.6 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: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_4981_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_4981_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_4981_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Spinach Cytochrome b6f complex with native bound plastoquinone an...
+Supramolecule #1: Spinach Cytochrome b6f complex with native bound plastoquinone an...
+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: BETA-CAROTENE
+Macromolecule #13: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #14: (4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-...
+Macromolecule #15: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #16: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #17: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #18: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 281 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN 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 K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.15 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |