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- PDB-7eyd: Cryo-EM structure of cyanobacterial phycobilisome from Anabaena s... -
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Basic information
Entry | Database: PDB / ID: 7eyd | ||||||
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Title | Cryo-EM structure of cyanobacterial phycobilisome from Anabaena sp. PCC 7120 | ||||||
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![]() | PHOTOSYNTHESIS | ||||||
Function / homology | ![]() Lyases / : / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
![]() | Zheng, L. / Zheng, Z. / Li, X. / Wang, G. / Zhang, K. / Wei, P. / Zhao, J. / Gao, N. | ||||||
Funding support | 1items
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![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 7.8 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
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-Validation report
Summary document | ![]() | 22.2 MB | Display | ![]() |
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Full document | ![]() | 30.8 MB | Display | |
Data in XML | ![]() | 1.3 MB | Display | |
Data in CIF | ![]() | 1.6 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31381MC ![]() 7extC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Phycobilisome ... , 5 types, 24 molecules A1A4N1N2N3N4N5N6N7NAA2A5A6AAA3A7G8N8U8b8i8293949
#1: Protein | Mass: 28688.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / Gene: cpcG2 / Production host: ![]() #4: Protein | Mass: 32254.086 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / Gene: cpcC, alr0530 / Production host: ![]() #5: Protein | Mass: 29362.826 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / Gene: cpcG4 / Production host: ![]() #6: Protein | Mass: 31973.932 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / Gene: cpcG1 / Production host: ![]() #9: Protein | Mass: 7852.082 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / Gene: apcC / Production host: ![]() |
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-C-phycocyanin ... , 2 types, 168 molecules B1D1F1H1J1L1O1Q1S1U1W1Y1B2D2F2H2J2L2O2Q2S2U2W2Y2B3D3F3H3J3L3...
#2: Protein | Mass: 17475.451 Da / Num. of mol.: 84 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / Gene: cpcA / Production host: ![]() #3: Protein | Mass: 18403.758 Da / Num. of mol.: 84 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / Gene: cpcB / Production host: ![]() |
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-Allophycocyanin subunit ... , 4 types, 94 molecules A8C8E8H8J8L8O8Q8S8V8X8Z8c8e8g8j8l8n8p8r8t8A9C9E9G9I9K9N9P9R9...
#7: Protein | Mass: 17362.617 Da / Num. of mol.: 44 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / Gene: apcA1 / Production host: ![]() #8: Protein | Mass: 17320.695 Da / Num. of mol.: 46 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / Gene: apcB / Production host: ![]() #11: Protein | Mass: 18657.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / Gene: apcF / Production host: ![]() #12: Protein | Mass: 17828.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / Gene: apcD / Production host: ![]() |
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-Protein / Non-polymers , 2 types, 350 molecules 0919![](data/chem/img/CYC.gif)
![](data/chem/img/CYC.gif)
#10: Protein | Mass: 127045.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / Gene: apcE / Production host: ![]() #13: Chemical | ChemComp-CYC / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Cryo-EM structure of cyanobacterial phycobilisome from Anabaena sp. PCC 7120 Type: COMPLEX / Entity ID: #1-#12 / Source: NATURAL |
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Molecular weight | Value: 7 MDa |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62439 / Symmetry type: POINT |