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Yorodumi- EMDB-31483: Cryo-EM structure of cyanobacterial PBS(delete Lr) from Synechoco... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31483 | |||||||||
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Title | Cryo-EM structure of cyanobacterial PBS(delete Lr) from Synechococcus sp.PCC 7002 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Lyases / : / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity Similarity search - Function | |||||||||
Biological species | Synechococcus sp. PCC 7002 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Zheng L / Zheng Z / Li X / Wang G / Zhang K / Wei P / Zhao J / Gao N | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural insight into the mechanism of energy transfer in cyanobacterial phycobilisomes. Authors: Lvqin Zheng / Zhenggao Zheng / Xiying Li / Guopeng Wang / Kun Zhang / Peijun Wei / Jindong Zhao / Ning Gao / Abstract: Phycobilisomes (PBS) are the major light-harvesting machineries for photosynthesis in cyanobacteria and red algae and they have a hierarchical structure of a core and peripheral rods, with both ...Phycobilisomes (PBS) are the major light-harvesting machineries for photosynthesis in cyanobacteria and red algae and they have a hierarchical structure of a core and peripheral rods, with both consisting of phycobiliproteins and linker proteins. Here we report the cryo-EM structures of PBS from two cyanobacterial species, Anabaena 7120 and Synechococcus 7002. Both PBS are hemidiscoidal in shape and share a common triangular core structure. While the Anabaena PBS has two additional hexamers in the core linked by the 4th linker domain of ApcE (L). The PBS structures predict that, compared with the PBS from red algae, the cyanobacterial PBS could have more direct routes for energy transfer to ApcD. Structure-based systematic mutagenesis analysis of the chromophore environment of ApcD and ApcF subunits reveals that aromatic residues are critical to excitation energy transfer (EET). The structures also suggest that the linker protein could actively participate in the process of EET in both rods and the cores. These results provide insights into the organization of chromophores and the mechanisms of EET within cyanobacterial PBS. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31483.map.gz | 26.3 MB | EMDB map data format | |
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Header (meta data) | emd-31483-v30.xml emd-31483.xml | 8.1 KB 8.1 KB | Display Display | EMDB header |
Images | emd_31483.png | 84.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31483 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31483 | HTTPS FTP |
-Validation report
Summary document | emd_31483_validation.pdf.gz | 343.8 KB | Display | EMDB validaton report |
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Full document | emd_31483_full_validation.pdf.gz | 343.4 KB | Display | |
Data in XML | emd_31483_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_31483_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31483 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31483 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_31483.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.052 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : cyanobacterial PBS(delete Lr) from Synechococcus sp.PCC 7002
Entire | Name: cyanobacterial PBS(delete Lr) from Synechococcus sp.PCC 7002 |
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Components |
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-Supramolecule #1: cyanobacterial PBS(delete Lr) from Synechococcus sp.PCC 7002
Supramolecule | Name: cyanobacterial PBS(delete Lr) from Synechococcus sp.PCC 7002 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Synechococcus sp. PCC 7002 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70852 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: PROJECTION MATCHING |