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Yorodumi- EMDB-36037: Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36037 | |||||||||
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Title | Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI in state 2 (PSI-ST2) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | photosystem / PLANT PROTEIN / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast stromal thylakoid / chloroplast photosystem I / response to low light intensity stimulus / chloroplast membrane / response to high light intensity / plastoglobule / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I ...photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast stromal thylakoid / chloroplast photosystem I / response to low light intensity stimulus / chloroplast membrane / response to high light intensity / plastoglobule / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / chloroplast envelope / thylakoid / photosystem I / photosynthetic electron transport in photosystem I / plastid / chloroplast thylakoid membrane / chlorophyll binding / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / extracellular region / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.22 Å | |||||||||
Authors | Chen SJB / Wu JH / Sui SF / Zhang LX | |||||||||
Funding support | China, 1 items
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Citation | Journal: Mol Plant / Year: 2023 Title: Regulatory dynamics of the higher-plant PSI-LHCI supercomplex during state transitions. Authors: Jianghao Wu / Shuaijiabin Chen / Chao Wang / Weijun Lin / Chao Huang / Chengxu Fan / Dexian Han / Dandan Lu / Xiumei Xu / SenFang Sui / Lixin Zhang / Abstract: State transition is a fundamental light acclimation mechanism of photosynthetic organisms in response to the environmental light conditions. This process rebalances the excitation energy between ...State transition is a fundamental light acclimation mechanism of photosynthetic organisms in response to the environmental light conditions. This process rebalances the excitation energy between photosystem I (PSI) and photosystem II through regulated reversible binding of the light-harvesting complex II (LHCII) to PSI. However, the structural reorganization of PSI-LHCI, the dynamic binding of LHCII, and the regulatory mechanisms underlying state transitions are less understood in higher plants. In this study, using cryoelectron microscopy we resolved the structures of PSI-LHCI in both state 1 (PSI-LHCI-ST1) and state 2 (PSI-LHCI-LHCII-ST2) from Arabidopsis thaliana. Combined genetic and functional analyses revealed novel contacts between Lhcb1 and PsaK that further enhanced the binding of the LHCII trimer to the PSI core with the known interactions between phosphorylated Lhcb2 and the PsaL/PsaH/PsaO subunits. Specifically, PsaO was absent in the PSI-LHCI-ST1 supercomplex but present in the PSI-LHCI-LHCII-ST2 supercomplex, in which the PsaL/PsaK/PsaA subunits undergo several conformational changes to strengthen the binding of PsaO in ST2. Furthermore, the PSI-LHCI module adopts a more compact configuration with shorter Mg-to-Mg distances between the chlorophylls, which may enhance the energy transfer efficiency from the peripheral antenna to the PSI core in ST2. Collectively, our work provides novel structural and functional insights into the mechanisms of light acclimation during state transitions in higher plants. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36037.map.gz | 129 MB | EMDB map data format | |
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Header (meta data) | emd-36037-v30.xml emd-36037.xml | 31.2 KB 31.2 KB | Display Display | EMDB header |
Images | emd_36037.png | 39.8 KB | ||
Filedesc metadata | emd-36037.cif.gz | 9.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36037 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36037 | HTTPS FTP |
-Validation report
Summary document | emd_36037_validation.pdf.gz | 549.2 KB | Display | EMDB validaton report |
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Full document | emd_36037_full_validation.pdf.gz | 548.7 KB | Display | |
Data in XML | emd_36037_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_36037_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36037 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36037 | HTTPS FTP |
-Related structure data
Related structure data | 8j7bMC 8j6zC 8j7aC C: citing same article (ref.) M: atomic model generated by this map |
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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_36037.map.gz / Format: CCP4 / Size: 144.7 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: 1.087 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-L...
+Supramolecule #1: Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-L...
+Macromolecule #1: Chlorophyll a-b binding protein 6, chloroplastic
+Macromolecule #2: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
+Macromolecule #3: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
+Macromolecule #4: Chlorophyll a-b binding protein 4, chloroplastic
+Macromolecule #5: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #6: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #7: Photosystem I iron-sulfur center
+Macromolecule #8: Photosystem I reaction center subunit II-2, chloroplastic
+Macromolecule #9: Photosystem I reaction center subunit IV A, chloroplastic
+Macromolecule #10: Photosystem I reaction center subunit III, chloroplastic
+Macromolecule #11: Photosystem I reaction center subunit V, chloroplastic
+Macromolecule #12: Photosystem I reaction center subunit VI-2, 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, chloroplastic
+Macromolecule #16: Photosystem I reaction center subunit XI, chloroplastic
+Macromolecule #17: CHLOROPHYLL B
+Macromolecule #18: CHLOROPHYLL A
+Macromolecule #19: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #20: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #21: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #22: BETA-CAROTENE
+Macromolecule #23: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #24: CHLOROPHYLL A ISOMER
+Macromolecule #25: PHYLLOQUINONE
+Macromolecule #26: IRON/SULFUR CLUSTER
+Macromolecule #27: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137602 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |