+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35018 | |||||||||
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Title | Cryo-EM structure of PpPSI-L | |||||||||
Map data | Combining three focused refinement maps, smPSI, LHCII and outer LHCI plus Lhcb9 | |||||||||
Sample |
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Keywords | Lhcb9 / PSI / PHOTOSYNTHESIS | |||||||||
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 / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Physcomitrium patens (plant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||
Authors | Li M / Pan XW / Sun HY | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Plants / Year: 2023 Title: Structural insights into the assembly and energy transfer of the Lhcb9-dependent photosystem I from moss Physcomitrium patens. Authors: Haiyu Sun / Hui Shang / Xiaowei Pan / Mei Li / Abstract: In plants and green algae, light-harvesting complexes I and II (LHCI and LHCII) constitute the antennae of photosystem I (PSI), thus effectively increasing the cross-section of the PSI core. The moss ...In plants and green algae, light-harvesting complexes I and II (LHCI and LHCII) constitute the antennae of photosystem I (PSI), thus effectively increasing the cross-section of the PSI core. The moss Physcomitrium patens (P. patens) represents a well-studied primary land-dwelling photosynthetic autotroph branching from the common ancestor of green algae and land plants at the early stage of evolution. P. patens possesses at least three types of PSI with different antenna sizes. The largest PSI form (PpPSI-L) exhibits a unique organization found neither in flowering plants nor in algae. Its formation is mediated by the P. patens-specific LHC protein, Lhcb9. While previous studies have revealed the overall architecture of PpPSI-L, its assembly details and the relationship between different PpPSI types remain unclear. Here we report the high-resolution structure of PpPSI-L. We identified 14 PSI core subunits, one Lhcb9, one phosphorylated LHCII trimer and eight LHCI monomers arranged as two belts. Our structural analysis established the essential role of Lhcb9 and the phosphorylated LHCII in stabilizing the complex. In addition, our results suggest that PpPSI switches between different types, which share identical modules. This feature may contribute to the dynamic adjustment of the light-harvesting capability of PSI under different light conditions. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35018.map.gz | 5.4 MB | EMDB map data format | |
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Header (meta data) | emd-35018-v30.xml emd-35018.xml | 36 KB 36 KB | Display Display | EMDB header |
Images | emd_35018.png | 140.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35018 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35018 | HTTPS FTP |
-Validation report
Summary document | emd_35018_validation.pdf.gz | 433.6 KB | Display | EMDB validaton report |
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Full document | emd_35018_full_validation.pdf.gz | 433.1 KB | Display | |
Data in XML | emd_35018_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_35018_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35018 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35018 | HTTPS FTP |
-Related structure data
Related structure data | 8htuMC 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_35018.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Combining three focused refinement maps, smPSI, LHCII and outer LHCI plus Lhcb9 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : photosystem I from Physcomitrium patens
+Supramolecule #1: photosystem I from Physcomitrium patens
+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: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #6: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #7: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #8: Photosystem I iron-sulfur center
+Macromolecule #9: Photosystem I reaction center subunit II, chloroplastic
+Macromolecule #10: Photosystem I reaction center subunit IV, chloroplastic
+Macromolecule #11: Photosystem I reaction center subunit III
+Macromolecule #12: Photosystem I reaction center subunit V, chloroplastic
+Macromolecule #13: Photosystem I reaction center subunit VI, chloroplastic
+Macromolecule #14: Photosystem I reaction center subunit VIII
+Macromolecule #15: Photosystem I reaction center subunit IX
+Macromolecule #16: Photosystem I subunit X
+Macromolecule #17: PSI subunit V
+Macromolecule #18: Photosystem I reaction center subunit XII
+Macromolecule #19: Photosystem I subunit O
+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: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...
+Macromolecule #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #27: BETA-CAROTENE
+Macromolecule #28: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #29: PHYLLOQUINONE
+Macromolecule #30: IRON/SULFUR CLUSTER
+Macromolecule #31: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #32: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #33: water
-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 TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: 5ZJI 7D0J |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144586 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |