[English] 日本語
![](img/lk-miru.gif)
- PDB-6kmw: Structure of PSI from H. hongdechloris grown under white light co... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6kmw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of PSI from H. hongdechloris grown under white light condition | |||||||||
![]() |
| |||||||||
![]() | ELECTRON TRANSPORT / Photosystem I | |||||||||
Function / homology | ![]() 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 ...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 | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å | |||||||||
![]() | Kato, K. / Nagao, R. / Shen, J.R. / Miyazaki, N. / Akita, F. | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 15.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 16.9 MB | Display | |
Data in XML | ![]() | 337.6 KB | Display | |
Data in CIF | ![]() | 431.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0726MC ![]() 0727C ![]() 6kmxC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
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) ![]() References: UniProt: A0A1Z3HRW4, photosystem I #2: Protein | Mass: 83080.469 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0A1Z3HRY4, photosystem I |
---|
-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) ![]() References: UniProt: A0A1Z3HHI7, photosystem I #5: Protein | Mass: 7907.028 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0A1Z3HI16 #6: Protein/peptide | Mass: 4318.124 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0A1Z3HSF0, photosystem I #7: Protein | Mass: 16871.471 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() 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) ![]() |
---|
-Protein / Sugars , 2 types, 6 molecules aCbCcC![](data/chem/img/LMT.gif)
![](data/chem/img/LMT.gif)
#15: Sugar | #3: Protein | Mass: 8782.184 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A0A1Z3HPE3, photosystem I |
---|
-Non-polymers , 10 types, 990 molecules ![](data/chem/img/CL0.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#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 / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
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 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Buffer solution | pH: 6.5 | |||||||||||||||
Buffer component |
| |||||||||||||||
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 |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
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 |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |