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Yorodumi- EMDB-35033: OutLHCIs plus Lhcb9 moiety of Large Photosystem I from Physcomitr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35033 | |||||||||||||||
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Title | OutLHCIs plus Lhcb9 moiety of Large Photosystem I from Physcomitrium patens | |||||||||||||||
Map data | Focused refinement map of the outLHCIs plus Lhcb9 moiety of PpPSI-L | |||||||||||||||
Sample |
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Keywords | Photosystem I / Lhcb9 / PHOTOSYNTHESIS | |||||||||||||||
Biological species | Physcomitrium patens (plant) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.29 Å | |||||||||||||||
Authors | Sun HY / Li M / Pan XW | |||||||||||||||
Funding support | China, 4 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_35033.map.gz | 7.5 MB | EMDB map data format | |
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Header (meta data) | emd-35033-v30.xml emd-35033.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
Images | emd_35033.png | 89.2 KB | ||
Others | emd_35033_half_map_1.map.gz emd_35033_half_map_2.map.gz | 98.5 MB 98.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35033 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35033 | HTTPS FTP |
-Validation report
Summary document | emd_35033_validation.pdf.gz | 771.3 KB | Display | EMDB validaton report |
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Full document | emd_35033_full_validation.pdf.gz | 770.9 KB | Display | |
Data in XML | emd_35033_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | emd_35033_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35033 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35033 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35033.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Focused refinement map of the outLHCIs plus Lhcb9 moiety of PpPSI-L | ||||||||||||||||||||
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
-Half map: #2
File | emd_35033_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35033_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Outer LHCIs plus Lhcb9 moiety of Large Photosystem I from Physcom...
Entire | Name: Outer LHCIs plus Lhcb9 moiety of Large Photosystem I from Physcomitrium patens |
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Components |
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-Supramolecule #1: Outer LHCIs plus Lhcb9 moiety of Large Photosystem I from Physcom...
Supramolecule | Name: Outer LHCIs plus Lhcb9 moiety of Large Photosystem I from Physcomitrium patens type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Physcomitrium patens (plant) |
-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: 7KSQ |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 89945 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |