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- PDB-8hfq: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hfq | ||||||
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Title | Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803 | ||||||
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![]() | PHOTOSYNTHESIS / CpcL-phycobilisome / energy transfer / ferredoxin:NADP+ oxidoreductase / ultrafast spectroscopy | ||||||
Function / homology | ![]() ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å | ||||||
![]() | Zheng, L. / Zhang, Z. / Wang, H. / Zheng, Z. / Gao, N. / Zhao, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM and femtosecond spectroscopic studies provide mechanistic insight into the energy transfer in CpcL-phycobilisomes. Authors: Lvqin Zheng / Zhengdong Zhang / Hongrui Wang / Zhenggao Zheng / Jiayu Wang / Heyuan Liu / Hailong Chen / Chunxia Dong / Guopeng Wang / Yuxiang Weng / Ning Gao / Jindong Zhao / ![]() Abstract: Phycobilisomes (PBS) are the major light harvesting complexes of photosynthesis in the cyanobacteria and red algae. CpcL-PBS is a type of small PBS in cyanobacteria that transfers energy directly to ...Phycobilisomes (PBS) are the major light harvesting complexes of photosynthesis in the cyanobacteria and red algae. CpcL-PBS is a type of small PBS in cyanobacteria that transfers energy directly to photosystem I without the core structure. Here we report the cryo-EM structure of the CpcL-PBS from the cyanobacterium Synechocystis sp. PCC 6803 at 2.6-Å resolution. The structure shows the CpcD domain of ferredoxin: NADP oxidoreductase is located at the distal end of CpcL-PBS, responsible for its attachment to PBS. With the evidence of ultrafast transient absorption and fluorescence spectroscopy, the roles of individual bilins in energy transfer are revealed. The bilin β located near photosystem I has an enhanced planarity and is the red-bilin responsible for the direct energy transfer to photosystem I. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 972.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.1 MB | Display | ![]() |
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Full document | ![]() | 4.3 MB | Display | |
Data in XML | ![]() | 203.4 KB | Display | |
Data in CIF | ![]() | 266.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34724MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-C-phycocyanin ... , 2 types, 36 molecules ACEGIKMOQSUWYacegiBDFHJLNPRTVX...
#1: Protein | Mass: 17602.529 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cpcA, sll1578 / Production host: ![]() ![]() #2: Protein | Mass: 18142.426 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cpcB, sll1577 / Production host: ![]() ![]() |
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-Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod ... , 2 types, 2 molecules kl
#3: Protein | Mass: 32558.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cpcC1, sll1580 / Production host: ![]() ![]() |
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#4: Protein | Mass: 30836.346 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cpcC2, sll1579 / Production host: ![]() ![]() |
-Protein , 2 types, 2 molecules mn
#5: Protein | Mass: 46417.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: petH, slr1643 / Production host: ![]() ![]() |
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#6: Protein | Mass: 28551.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cpcL, cpcG2, sll1471 / Production host: ![]() ![]() |
-Non-polymers , 1 types, 54 molecules ![](data/chem/img/CYC.gif)
#7: 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 CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803 Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803 |
Vitrification | 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 / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124441 / Symmetry type: POINT |