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Yorodumi- PDB-6kmx: Structure of PSI from H. hongdechloris grown under far-red light ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kmx | |||||||||
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Title | Structure of PSI from H. hongdechloris grown under far-red light condition | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / Photosystem I | |||||||||
Function / homology | Function and homology information thylakoid membrane / : / photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding ...thylakoid membrane / : / photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / oxidoreductase activity / electron transfer 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: 2.41 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 | 6kmx.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6kmx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6kmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kmx_validation.pdf.gz | 16.2 MB | Display | wwPDB validaton report |
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Full document | 6kmx_full_validation.pdf.gz | 17.4 MB | Display | |
Data in XML | 6kmx_validation.xml.gz | 340.2 KB | Display | |
Data in CIF | 6kmx_validation.cif.gz | 434.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/6kmx ftp://data.pdbj.org/pub/pdb/validation_reports/km/6kmx | HTTPS FTP |
-Related structure data
Related structure data | 0727MC 0726C 6kmwC C: citing same article (ref.) M: map data used to model this data |
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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: 87406.258 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) References: UniProt: A0A1Z3HIN6, photosystem I #2: Protein | Mass: 83287.695 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) References: UniProt: A0A1Z3HIL0, photosystem I |
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-Photosystem I reaction center subunit ... , 6 types, 18 molecules aDbDcDaEbEcEaIbIcIaKbKcKaLbLcLaMbMcM
#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 | Mass: 7136.356 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) References: UniProt: A0A1Z3HIL5, photosystem I #7: Protein | Mass: 9726.539 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) References: UniProt: A0A1Z3HR36 #8: Protein | Mass: 20191.928 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Halomicronema hongdechloris C2206 (bacteria) References: UniProt: A0A1Z3HIQ7, photosystem I #9: 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
#17: 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 , 11 types, 996 molecules
#10: Chemical | #11: Chemical | ChemComp-CLA / #12: Chemical | ChemComp-F6C / Mass: 905.457 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C55H68MgN4O6 #13: Chemical | ChemComp-PQN / #14: Chemical | ChemComp-SF4 / #15: Chemical | ChemComp-BCR / #16: Chemical | #18: Chemical | #19: Chemical | ChemComp-UNL / Num. of mol.: 15 / Source method: obtained synthetically #20: Chemical | #21: 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: far-red PSI / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL | ||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||
Source (natural) | Organism: Halomicronema hongdechloris (bacteria) | ||||||||||||
Buffer solution | pH: 6.5 | ||||||||||||
Buffer component |
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Specimen | Conc.: 0.071 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: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 311993 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient | ||||||||||||||||
Atomic model building | PDB-ID: 1JB0 Accession code: 1JB0 / Source name: PDB / Type: experimental model |