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Yorodumi- EMDB-30925: State transition supercomplex PSI-LHCI-LHCII from double phosphat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30925 | |||||||||||||||||||||||||||
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Title | State transition supercomplex PSI-LHCI-LHCII from double phosphatase mutant pph1;pbcp of green alga Chlamydomonas reinhardtii | |||||||||||||||||||||||||||
Map data | ||||||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane ...photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) / Chlamydomonas smithii (plant) | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||||||||||||||||||||
Authors | Pan XW / Li AJ / Liu ZF / Li M | |||||||||||||||||||||||||||
Funding support | China, Japan, 8 items
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Citation | Journal: Nat Plants / Year: 2021 Title: Structural basis of LhcbM5-mediated state transitions in green algae. Authors: Xiaowei Pan / Ryutaro Tokutsu / Anjie Li / Kenji Takizawa / Chihong Song / Kazuyoshi Murata / Tomohito Yamasaki / Zhenfeng Liu / Jun Minagawa / Mei Li / Abstract: In green algae and plants, state transitions serve as a short-term light-acclimation process in the regulation of the light-harvesting capacity of photosystems I and II (PSI and PSII, respectively). ...In green algae and plants, state transitions serve as a short-term light-acclimation process in the regulation of the light-harvesting capacity of photosystems I and II (PSI and PSII, respectively). During the process, a portion of light-harvesting complex II (LHCII) is phosphorylated, dissociated from PSII and binds with PSI to form the supercomplex PSI-LHCI-LHCII. Here, we report high-resolution structures of PSI-LHCI-LHCII from Chlamydomonas reinhardtii, revealing the mechanism of assembly between the PSI-LHCI complex and two phosphorylated LHCII trimers containing all four types of LhcbM protein. Two specific LhcbM isoforms, namely LhcbM1 and LhcbM5, directly interact with the PSI core through their phosphorylated amino terminal regions. Furthermore, biochemical and functional studies on mutant strains lacking either LhcbM1 or LhcbM5 indicate that only LhcbM5 is indispensable in supercomplex formation. The results unravel the specific interactions and potential excitation energy transfer routes between green algal PSI and two phosphorylated LHCIIs. | |||||||||||||||||||||||||||
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_30925.map.gz | 29.6 MB | EMDB map data format | |
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Header (meta data) | emd-30925-v30.xml emd-30925.xml | 40.6 KB 40.6 KB | Display Display | EMDB header |
Images | emd_30925.png | 439 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30925 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30925 | HTTPS FTP |
-Validation report
Summary document | emd_30925_validation.pdf.gz | 340.6 KB | Display | EMDB validaton report |
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Full document | emd_30925_full_validation.pdf.gz | 340.2 KB | Display | |
Data in XML | emd_30925_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_30925_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30925 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30925 | HTTPS FTP |
-Related structure data
Related structure data | 7dz7MC 7dz8C 7e0hC 7e0iC 7e0jC 7e0kC 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_30925.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1 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 : State transition complex PSI-LHCI-LHCII from green algae
+Supramolecule #1: State transition complex PSI-LHCI-LHCII from green algae
+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 V, chloroplastic
+Macromolecule #8: Photosystem I reaction center subunit VI, chloroplastic
+Macromolecule #9: Photosystem I reaction center subunit VIII
+Macromolecule #10: Photosystem I reaction center subunit IX
+Macromolecule #11: Photosystem I reaction center subunit psaK, chloroplastic
+Macromolecule #12: PSI subunit V
+Macromolecule #13: Photosystem I subunit O
+Macromolecule #14: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #15: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #16: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #17: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #18: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #19: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #20: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #21: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #22: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #23: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #24: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #25: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #26: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #27: CHLOROPHYLL A
+Macromolecule #28: PHYLLOQUINONE
+Macromolecule #29: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #30: BETA-CAROTENE
+Macromolecule #31: IRON/SULFUR CLUSTER
+Macromolecule #32: DODECYL-ALPHA-D-MALTOSIDE
+Macromolecule #33: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #34: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #35: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #36: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #37: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...
+Macromolecule #38: CHLOROPHYLL B
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5625 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56601 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |