+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33558 | |||||||||
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Title | Lateral hexamer | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / phycobilisome / chloroplast thylakoid membrane / photosynthesis / Globin-like superfamily / Phycoerythrin alpha subunit / B-phycoerythrin beta chain Function and homology information | |||||||||
Biological species | Porphyridium purpureum (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.3 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_33558.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-33558-v30.xml emd-33558.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_33558.png | 65.7 KB | ||
Others | emd_33558_half_map_1.map.gz emd_33558_half_map_2.map.gz | 58.5 MB 58.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33558 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33558 | HTTPS FTP |
-Related structure data
Related structure data | 7y1aMC 7y4lC 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_33558.map.gz / Format: CCP4 / Size: 64 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: #1
File | emd_33558_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33558_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Lateral hexamer of PBS
Entire | Name: Lateral hexamer of PBS |
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Components |
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-Supramolecule #1: Lateral hexamer of PBS
Supramolecule | Name: Lateral hexamer of PBS / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Porphyridium purpureum (eukaryote) |
-Macromolecule #1: B-phycoerythrin beta chain
Macromolecule | Name: B-phycoerythrin beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Porphyridium purpureum (eukaryote) |
Molecular weight | Theoretical: 18.584182 KDa |
Recombinant expression | Organism: Porphyridium purpureum (eukaryote) |
Sequence | String: MLDAFSRVVV NSDAKAAYVG GSDLQALKSF IADGNKRLDA VNSIVSNASC MVSDAVSGMI CENPGLISPG G(MEN)CYTN RRM AACLRDGEII LRYVSYALLA GDASVLEDRC LNGLKETYIA LGVPTNSSIR AVSIMKAQAV AFITNTATER KMSFAAG DC TSLASEVASY FDRVGAAIS |
-Macromolecule #2: Phycoerythrin alpha subunit
Macromolecule | Name: Phycoerythrin alpha subunit / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Porphyridium purpureum (eukaryote) |
Molecular weight | Theoretical: 17.824029 KDa |
Recombinant expression | Organism: Porphyridium purpureum (eukaryote) |
Sequence | String: MKSVITTVVS AADAAGRFPS NSDLESIQGN IQRSAARLEA AEKLAGNHEA VVKEAGDACF AKYAYLKNPG EAGENQEKIN KCYRDVDHY MRLVNYCLVV GGTGPLDEWG IAGAREVYRT LNLPTSAYVA SIAYTRDRLC VPRDMSAQAG VEFSAYLDYL I NALS |
-Macromolecule #3: LRH
Macromolecule | Name: LRH / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Porphyridium purpureum (eukaryote) |
Molecular weight | Theoretical: 7.42214 KDa |
Recombinant expression | Organism: Porphyridium purpureum (eukaryote) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) |
-Macromolecule #4: LRH
Macromolecule | Name: LRH / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Porphyridium purpureum (eukaryote) |
Molecular weight | Theoretical: 12.78375 KDa |
Recombinant expression | Organism: Porphyridium purpureum (eukaryote) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #5: PHYCOERYTHROBILIN
Macromolecule | Name: PHYCOERYTHROBILIN / type: ligand / ID: 5 / Number of copies: 31 / Formula: PEB |
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Molecular weight | Theoretical: 588.694 Da |
Chemical component information | ChemComp-PEB: |
-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: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |