+Open data
-Basic information
Entry | Database: PDB / ID: 6l4t | ||||||
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Title | Structure of the peripheral FCPI from diatom | ||||||
Components | (Fucoxanthin chlorophyll a/c-binding protein ...) x 10 | ||||||
Keywords | ELECTRON TRANSPORT / Photosystem I | ||||||
Function / homology | Chem-A86 / CHLOROPHYLL A / Chem-DD6 / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE Function and homology information | ||||||
Biological species | Chaetoceros gracilis (Diatom) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Nagao, R. / Kato, K. / Miyazaki, N. / Akita, F. / Shen, J.R. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex. Authors: Ryo Nagao / Koji Kato / Kentaro Ifuku / Takehiro Suzuki / Minoru Kumazawa / Ikuo Uchiyama / Yasuhiro Kashino / Naoshi Dohmae / Seiji Akimoto / Jian-Ren Shen / Naoyuki Miyazaki / Fusamichi Akita / Abstract: Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c- ...Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c-binding proteins (FCPs) present in diatoms, a group of organisms having important contribution to the global carbon cycle. Here, we report a 2.40-Å resolution structure of the diatom photosystem I (PSI)-FCPI supercomplex by cryo-electron microscopy. The supercomplex is composed of 16 different FCPI subunits surrounding a monomeric PSI core. Each FCPI subunit showed different protein structures with different pigment contents and binding sites, and they form a complicated pigment-protein network together with the PSI core to harvest and transfer the light energy efficiently. In addition, two unique, previously unidentified subunits were found in the PSI core. The structure provides numerous insights into not only the light-harvesting strategy in diatom PSI-FCPI but also evolutionary dynamics of light harvesters among oxyphototrophs. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6l4t.cif.gz | 555.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l4t.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6l4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l4t_validation.pdf.gz | 9.6 MB | Display | wwPDB validaton report |
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Full document | 6l4t_full_validation.pdf.gz | 10.6 MB | Display | |
Data in XML | 6l4t_validation.xml.gz | 208.2 KB | Display | |
Data in CIF | 6l4t_validation.cif.gz | 237.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/6l4t ftp://data.pdbj.org/pub/pdb/validation_reports/l4/6l4t | HTTPS FTP |
-Related structure data
Related structure data | 0834MC 0835C 6l4uC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Fucoxanthin chlorophyll a/c-binding protein ... , 10 types, 10 molecules 67810111213141516
#1: Protein | Mass: 22362.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
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#2: Protein | Mass: 32238.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
#3: Protein | Mass: 29704.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
#4: Protein | Mass: 22216.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
#5: Protein | Mass: 24842.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
#6: Protein | Mass: 21318.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
#7: Protein | Mass: 25994.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
#8: Protein | Mass: 26875.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
#9: Protein | Mass: 30545.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
#10: Protein | Mass: 23533.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) |
-Sugars , 1 types, 13 molecules
#17: Sugar | ChemComp-LMT / |
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-Non-polymers , 7 types, 191 molecules
#11: Chemical | ChemComp-CLA / #12: Chemical | ChemComp-KC1 / #13: Chemical | ChemComp-DD6 / ( #14: Chemical | ChemComp-A86 / ( #15: Chemical | ChemComp-LHG / | #16: Chemical | ChemComp-LMG / #18: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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 |
-Sample preparation
Component | Name: peripheral FCPI / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.17 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Chaetoceros gracilis (Diatom) | |||||||||||||||
Buffer solution | pH: 6.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: MOLYBDENUM / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2689965 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 470801 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |