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Yorodumi- EMDB-6932: Structure of photosystem I supercomplex with light-harvesting com... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6932 | |||||||||||||||||||||||||||||||||
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Title | Structure of photosystem I supercomplex with light-harvesting complexes I and II | |||||||||||||||||||||||||||||||||
Map data | ||||||||||||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information thylakoid membrane / photosynthesis, light harvesting / plastoglobule / photosynthesis, light harvesting in photosystem I / : / photosystem I reaction center / photosystem I / chloroplast envelope / photosystem I / photosystem II ...thylakoid membrane / photosynthesis, light harvesting / plastoglobule / photosynthesis, light harvesting in photosystem I / : / photosystem I reaction center / photosystem I / chloroplast envelope / photosystem I / photosystem II / plastid / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | Zea mays (maize) / Maize (maize) / maize (maize) | |||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||||||||||||||||||||
Authors | Pan XW / Ma J / Su XD / Cao P / Liu ZF / Zhang XZ / Li M | |||||||||||||||||||||||||||||||||
Funding support | China, 10 items
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Citation | Journal: Science / Year: 2018 Title: Structure of the maize photosystem I supercomplex with light-harvesting complexes I and II. Authors: Xiaowei Pan / Jun Ma / Xiaodong Su / Peng Cao / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li / Abstract: Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, light- ...Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, light-harvesting complex II (LHCII), is phosphorylated and forms a supercomplex with PSI core and the PSI antenna, light-harvesting complex I (LHCI). Both LHCI and LHCII then transfer excitation energy to the PSI core. We report the structure of maize PSI-LHCI-LHCII solved by cryo-electron microscopy, revealing the recognition site between LHCII and PSI. The PSI subunits PsaN and PsaO are observed at the PSI-LHCI interface and the PSI-LHCII interface, respectively. Each subunit relays excitation to PSI core through a pair of chlorophyll molecules, thus revealing previously unseen paths for energy transfer between the antennas and the PSI core. | |||||||||||||||||||||||||||||||||
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_6932.map.gz | 78 MB | EMDB map data format | |
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Header (meta data) | emd-6932-v30.xml emd-6932.xml | 34.7 KB 34.7 KB | Display Display | EMDB header |
Images | emd_6932.png | 129.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6932 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6932 | HTTPS FTP |
-Validation report
Summary document | emd_6932_validation.pdf.gz | 577.8 KB | Display | EMDB validaton report |
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Full document | emd_6932_full_validation.pdf.gz | 577.3 KB | Display | |
Data in XML | emd_6932_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_6932_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6932 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6932 | HTTPS FTP |
-Related structure data
Related structure data | 5zjiMC 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_6932.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 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 : Supercomplex of plant PSI-LHCI-LHCII from Zea Mays
+Supramolecule #1: Supercomplex of plant PSI-LHCI-LHCII from Zea Mays
+Macromolecule #1: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #2: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #4: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #5: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #6: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #7: photosystem I subunit VII
+Macromolecule #8: Photosystem I reaction center subunit II
+Macromolecule #9: Photosystem I reaction center subunit IV A
+Macromolecule #10: Photosystem I reaction center subunit III
+Macromolecule #11: Photosystem I reaction center subunit V
+Macromolecule #12: Photosystem I reaction center subunit VI, chloroplastic
+Macromolecule #13: Photosystem I reaction center subunit VIII
+Macromolecule #14: Photosystem I reaction center subunit IX
+Macromolecule #15: Photosystem I reaction center subunit psaK
+Macromolecule #16: Photosystem I reaction center subunit XI
+Macromolecule #17: 16kDa membrane protein
+Macromolecule #18: Photosystem I reaction center subunit N
+Macromolecule #19: Chlorophyll a-b binding protein 1, chloroplastic
+Macromolecule #20: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #21: CHLOROPHYLL B
+Macromolecule #22: CHLOROPHYLL A
+Macromolecule #23: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #24: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #25: BETA-CAROTENE
+Macromolecule #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #27: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #28: CHLOROPHYLL A ISOMER
+Macromolecule #29: PHYLLOQUINONE
+Macromolecule #30: IRON/SULFUR CLUSTER
+Macromolecule #31: DODECYL-ALPHA-D-MALTOSIDE
+Macromolecule #32: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #33: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 635845 |
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Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |