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Yorodumi- PDB-6kmw: Structure of PSI from H. hongdechloris grown under white light co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kmw | |||||||||
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Title | Structure of PSI from H. hongdechloris grown under white light condition | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / Photosystem I | |||||||||
Function / homology | Function and homology information photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Halomicronema hongdechloris C2206 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å | |||||||||
Authors | Kato, K. / Nagao, R. / Shen, J.R. / Miyazaki, N. / Akita, F. | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis for the adaptation and function of chlorophyll f in photosystem I. Authors: Koji Kato / Toshiyuki Shinoda / Ryo Nagao / Seiji Akimoto / Takehiro Suzuki / Naoshi Dohmae / Min Chen / Suleyman I Allakhverdiev / Jian-Ren Shen / Fusamichi Akita / Naoyuki Miyazaki / Tatsuya Tomo / Abstract: Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first ...Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f. | |||||||||
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 | 6kmw.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6kmw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6kmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kmw_validation.pdf.gz | 15.7 MB | Display | wwPDB validaton report |
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Full document | 6kmw_full_validation.pdf.gz | 16.9 MB | Display | |
Data in XML | 6kmw_validation.xml.gz | 337.6 KB | Display | |
Data in CIF | 6kmw_validation.cif.gz | 431.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/6kmw ftp://data.pdbj.org/pub/pdb/validation_reports/km/6kmw | HTTPS FTP |
-Related structure data
Related structure data | 0726MC 0727C 6kmxC 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
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 6 molecules aAbAcAaBbBcB
#1: Protein | Mass: 84273.633 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) References: UniProt: A0A1Z3HRW4, photosystem I #2: Protein | Mass: 83080.469 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) References: UniProt: A0A1Z3HRY4, photosystem I |
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-Photosystem I reaction center subunit ... , 5 types, 15 molecules aDbDcDaEbEcEaIbIcIaLbLcLaMbMcM
#4: Protein | Mass: 15723.800 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) References: UniProt: A0A1Z3HHI7, photosystem I #5: Protein | Mass: 7907.028 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) References: UniProt: A0A1Z3HI16 #6: Protein/peptide | Mass: 4318.124 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) References: UniProt: A0A1Z3HSF0, photosystem I #7: Protein | Mass: 16871.471 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) References: UniProt: A0A1Z3HS05, photosystem I #8: Protein/peptide | Mass: 3440.141 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) |
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-Protein / Sugars , 2 types, 6 molecules aCbCcC
#15: Sugar | #3: Protein | Mass: 8782.184 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) References: UniProt: A0A1Z3HPE3, photosystem I |
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-Non-polymers , 10 types, 990 molecules
#9: Chemical | #10: Chemical | ChemComp-CLA / #11: Chemical | ChemComp-PQN / #12: Chemical | ChemComp-SF4 / #13: Chemical | ChemComp-BCR / #14: Chemical | ChemComp-LHG / #16: Chemical | #17: Chemical | ChemComp-UNL / Num. of mol.: 15 / Source method: obtained synthetically #18: Chemical | #19: 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: white PSI / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Halomicronema hongdechloris C2206 (bacteria) | |||||||||||||||
Buffer solution | pH: 6.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.032 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
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: 47 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 | ||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||
3D reconstruction | Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 546366 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||
Atomic model building | PDB-ID: 1JB0 Accession code: 1JB0 / Source name: PDB / Type: experimental model |