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- PDB-8j0d: FCP heterodimer, Lhca2, and Lhcf5 together as the M1 side binds t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8j0d | ||||||
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Title | FCP heterodimer, Lhca2, and Lhcf5 together as the M1 side binds to the PSII core in the diatom Thalassiosira pseudonana | ||||||
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![]() | PHOTOSYNTHESIS / FCP / heterodimer | ||||||
Function / homology | ![]() light-harvesting complex / photosynthesis, light harvesting in photosystem I / plastid / chlorophyll binding / response to light stimulus / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å | ||||||
![]() | Li, Z. / Feng, Y. / Wang, W. / Shen, J.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a diatom photosystem II supercomplex containing a member of Lhcx family and dimeric FCPII. Authors: Yue Feng / Zhenhua Li / Xiaoyi Li / Lili Shen / Xueyang Liu / Cuicui Zhou / Jinyang Zhang / Min Sang / Guangye Han / Wenqiang Yang / Tingyun Kuang / Wenda Wang / Jian-Ren Shen / ![]() ![]() Abstract: Diatoms rely on fucoxanthin chlorophyll -binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We ...Diatoms rely on fucoxanthin chlorophyll -binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We report a unique structure of photosystem II (PSII)-FCPII supercomplex from at 2.68-Å resolution by cryo-electron microscopy. FCPIIs within this PSII-FCPII supercomplex exist in dimers and monomers, and a homodimer and a heterodimer were found to bind to a PSII core. The FCPII homodimer is formed by Lhcf7 and associates with PSII through an Lhcx family antenna Lhcx6_1, whereas the heterodimer is formed by Lhcf6 and Lhcf11 and connects to the core together with an Lhcf5 monomer through Lhca2 monomer. An extended pigment network consisting of diatoxanthins, diadinoxanthins, fucoxanthins, and chlorophylls is revealed, which functions in efficient light harvesting, energy transfer, and dissipation. These results provide a structural basis for revealing the energy transfer and dissipation mechanisms and also for the structural diversity of FCP antennas in diatoms. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.2 KB | Display | ![]() |
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PDB format | ![]() | 204.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.9 MB | Display | ![]() |
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Full document | ![]() | 5.1 MB | Display | |
Data in XML | ![]() | 81.1 KB | Display | |
Data in CIF | ![]() | 99.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35899MC ![]() 8iwhC 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
-Protein , 2 types, 2 molecules 34
#1: Protein | Mass: 24100.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 17745.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Fucoxanthin chlorophyll a/c protein ... , 2 types, 2 molecules 56
#3: Protein | Mass: 17614.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#4: Protein | Mass: 18380.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars , 2 types, 3 molecules ![](data/chem/img/DGD.gif)
![](data/chem/img/LMT.gif)
![](data/chem/img/LMT.gif)
#11: Sugar | ChemComp-DGD / |
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#13: Sugar |
-Non-polymers , 7 types, 71 molecules ![](data/chem/img/CLA.gif)
![](data/chem/img/KC1.gif)
![](data/chem/img/A86.gif)
![](data/chem/img/DD6.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/KC2.gif)
![](data/chem/img/KC1.gif)
![](data/chem/img/A86.gif)
![](data/chem/img/DD6.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/KC2.gif)
#5: Chemical | ChemComp-CLA / #6: Chemical | #7: Chemical | ChemComp-A86 / ( #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-LHG / #12: Chemical | |
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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: M1 local refinement in the PSII-FCPII from the Thalassiosira pseudonana at 3.19 angstrom Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: 2000 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
EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97098 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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