+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33605 | |||||||||
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Title | PBS of PBS-PSII-PSI-LHCs from Porphyridium purpureum. | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information phycobilisome / chloroplast thylakoid membrane / photosynthesis / cell adhesion molecule binding / extracellular matrix organization / extracellular matrix / macroautophagy / cell adhesion / lyase activity / extracellular space Similarity search - Function | |||||||||
Biological species | Porphyridium purpureum (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | You X / Zhang X / Cheng J / Xiao YN / Sun S / Sui SF | |||||||||
Funding support | 1 items
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Citation | Journal: Nature / Year: 2023 Title: In situ structure of the red algal phycobilisome-PSII-PSI-LHC megacomplex. Authors: Xin You / Xing Zhang / Jing Cheng / Yanan Xiao / Jianfei Ma / Shan Sun / Xinzheng Zhang / Hong-Wei Wang / Sen-Fang Sui / Abstract: In oxygenic photosynthetic organisms, light energy is captured by antenna systems and transferred to photosystem II (PSII) and photosystem I (PSI) to drive photosynthesis. The antenna systems of red ...In oxygenic photosynthetic organisms, light energy is captured by antenna systems and transferred to photosystem II (PSII) and photosystem I (PSI) to drive photosynthesis. The antenna systems of red algae consist of soluble phycobilisomes (PBSs) and transmembrane light-harvesting complexes (LHCs). Excitation energy transfer pathways from PBS to photosystems remain unclear owing to the lack of structural information. Here we present in situ structures of PBS-PSII-PSI-LHC megacomplexes from the red alga Porphyridium purpureum at near-atomic resolution using cryogenic electron tomography and in situ single-particle analysis, providing interaction details between PBS, PSII and PSI. The structures reveal several unidentified and incomplete proteins and their roles in the assembly of the megacomplex, as well as a huge and sophisticated pigment network. This work provides a solid structural basis for unravelling the mechanisms of PBS-PSII-PSI-LHC megacomplex assembly, efficient energy transfer from PBS to the two photosystems, and regulation of energy distribution between PSII and PSI. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33605.map.gz | 203.7 MB | EMDB map data format | |
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Header (meta data) | emd-33605-v30.xml emd-33605.xml | 50.4 KB 50.4 KB | Display Display | EMDB header |
Images | emd_33605.png | 183.6 KB | ||
Others | emd_33605_half_map_1.map.gz emd_33605_half_map_2.map.gz | 200.5 MB 200.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33605 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33605 | HTTPS FTP |
-Validation report
Summary document | emd_33605_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_33605_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_33605_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_33605_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33605 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33605 | HTTPS FTP |
-Related structure data
Related structure data | 7y4lMC 8jnnM 7y1aC 7y5eC 7y7aC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33605.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.632 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33605_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33605_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : In situ PBS from Porphyridium purpureum
+Supramolecule #1: In situ PBS from Porphyridium purpureum
+Macromolecule #1: Linker4
+Macromolecule #2: B-phycoerythrin beta chain
+Macromolecule #3: Phycoerythrin alpha subunit
+Macromolecule #4: CaRSPs1
+Macromolecule #5: CaRSPs2
+Macromolecule #6: R-phycoerythrin gamma chain, chloroplastic
+Macromolecule #7: Phycobilisome rod-core linker polypeptide
+Macromolecule #8: C-phycocyanin alpha subunit
+Macromolecule #9: C-phycocyanin beta subunit
+Macromolecule #10: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associat...
+Macromolecule #11: Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associat...
+Macromolecule #12: R-phycoerythrin gamma chain, chloroplastic
+Macromolecule #13: R-phycoerythrin gamma chain, chloroplastic
+Macromolecule #14: R-phycoerythrin gamma chain, chloroplastic
+Macromolecule #15: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associat...
+Macromolecule #16: Lrc4
+Macromolecule #17: LRC5
+Macromolecule #18: FAS1 domain-containing protein
+Macromolecule #19: Allophycocyanin alpha subunit
+Macromolecule #20: Allophycocyanin beta subunit
+Macromolecule #21: Allophycocyanin gamma subunit
+Macromolecule #22: Allophycocyanin beta 18 subunit
+Macromolecule #23: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...
+Macromolecule #24: Phycobiliprotein ApcE
+Macromolecule #25: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
+Macromolecule #26: Phycobilisome 27.9 kDa linker polypeptide, phycoerythrin-associat...
+Macromolecule #27: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associat...
+Macromolecule #28: Phycobilisome 31.8 kDa linker polypeptide, phycoerythrin-associat...
+Macromolecule #29: FAS1 domain-containing protein
+Macromolecule #30: LPP2
+Macromolecule #31: PHYCOERYTHROBILIN
+Macromolecule #32: PHYCOUROBILIN
+Macromolecule #33: PHYCOCYANOBILIN
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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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 K3 (6k x 4k) / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 215000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |