+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31498 | |||||||||
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Title | PSI-NDH supercomplex of Barley | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information NADH dehydrogenase complex (plastoquinone) assembly / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthesis, light harvesting / photosystem II oxygen evolving complex / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I ...NADH dehydrogenase complex (plastoquinone) assembly / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthesis, light harvesting / photosystem II oxygen evolving complex / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / thylakoid / photosystem I / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / photosystem II / extrinsic component of membrane / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis, light reaction / iron-sulfur cluster binding / response to light stimulus / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / defense response to fungus / catalytic activity / photosynthesis / chloroplast / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mitochondrial membrane / NAD binding / protein folding / 4 iron, 4 sulfur cluster binding / carbohydrate binding / response to oxidative stress / electron transfer activity / membrane => GO:0016020 / carbohydrate metabolic process / iron ion binding / calcium ion binding / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Hordeum vulgare subsp. spontaneum (wild barley) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Wang WD / Shen L / Tang K / Han GY / Shen JR / Zhang X | |||||||||
Funding support | China, 1 items
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Citation | Journal: Science / Year: 2015 Title: Photosynthesis. Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex. Authors: Xiaochun Qin / Michihiro Suga / Tingyun Kuang / Jian-Ren Shen / Abstract: Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by ...Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by a large light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core with extremely high efficiency. We report the structure of PSI-LHCI, a 600-kilodalton membrane protein supercomplex, from Pisum sativum (pea) at a resolution of 2.8 angstroms. The structure reveals the detailed arrangement of pigments and other cofactors—especially within LHCI—as well as numerous specific interactions between the PSI core and LHCI. These results provide a firm structural basis for our understanding on the energy transfer and photoprotection mechanisms within the PSI-LHCI supercomplex. | |||||||||
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_31498.map.gz | 304.1 MB | EMDB map data format | |
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Header (meta data) | emd-31498-v30.xml emd-31498.xml | 59.9 KB 59.9 KB | Display Display | EMDB header |
Images | emd_31498.png | 91.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31498 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31498 | HTTPS FTP |
-Related structure data
Related structure data | 7f9oMC 7eu3C 7ew6C 7ewkC 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_31498.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.307 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : PSI-NDH supercomplex of Barley
+Supramolecule #1: PSI-NDH supercomplex of Barley
+Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #3: Photosystem I iron-sulfur center
+Macromolecule #4: Photosystem I reaction center subunit II, chloroplastic
+Macromolecule #5: Photosystem I reaction center subunit IV, chloroplastic
+Macromolecule #6: Photosystem I reaction center subunit III, chloroplastic
+Macromolecule #7: Photosystem I reaction center subunit VI, chloroplastic
+Macromolecule #8: Photosystem I reaction center subunit VIII
+Macromolecule #9: Photosystem I reaction center subunit IX
+Macromolecule #10: Photosystem I reaction center subunit psaK, chloroplastic
+Macromolecule #11: Photosystem I reaction center subunit XI, chloroplastic
+Macromolecule #12: Chlorophyll a-b binding protein Lhca1
+Macromolecule #13: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #14: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #15: Chlorophyll a-b binding protein Lhca5
+Macromolecule #16: NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic
+Macromolecule #17: NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic
+Macromolecule #18: NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic
+Macromolecule #19: NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
+Macromolecule #20: NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic
+Macromolecule #21: NADH-plastoquinone oxidoreductase subunit 5
+Macromolecule #22: NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic
+Macromolecule #23: NAD(P)H-quinone oxidoreductase subunit H, chloroplastic
+Macromolecule #24: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
+Macromolecule #25: NAD(P)H-quinone oxidoreductase subunit J, chloroplastic
+Macromolecule #26: NAD(P)H-quinone oxidoreductase subunit K, chloroplastic
+Macromolecule #27: NAD(P)H-quinone oxidoreductase subunit L, chloroplastic
+Macromolecule #28: NAD(P)H-quinone oxidoreductase subunit M, chloroplastic
+Macromolecule #29: NAD(P)H-quinone oxidoreductase subunit N, chloroplastic
+Macromolecule #30: Unidentified stromal protein
+Macromolecule #31: Photosynthetic NDH subunit of subcomplex L1
+Macromolecule #32: Photosynthetic NDH subunit of subcomplex L2
+Macromolecule #33: Photosynthetic NDH subunit of subcomplex L2
+Macromolecule #34: Photosynthetic NDH subunit of subcomplex L4
+Macromolecule #35: Photosynthetic NDH subunit of subcomplex L5
+Macromolecule #36: Photosynthetic NDH subunit of subcomplex B1
+Macromolecule #37: Photosynthetic NDH subunit of subcomplex B2
+Macromolecule #38: Photosynthetic NDH subunit of subcomplex B3
+Macromolecule #39: Photosynthetic NDH subunit of subcomplex B4
+Macromolecule #40: Photosynthetic NDH subunit of subcomplex B5
+Macromolecule #41: Chlorophyll a-b binding protein Lhca4
+Macromolecule #42: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #43: CHLOROPHYLL A ISOMER
+Macromolecule #44: CHLOROPHYLL A
+Macromolecule #45: PHYLLOQUINONE
+Macromolecule #46: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #47: BETA-CAROTENE
+Macromolecule #48: IRON/SULFUR CLUSTER
+Macromolecule #49: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #50: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #51: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #52: CHLOROPHYLL B
+Macromolecule #53: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #54: 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: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103844 |