[English] 日本語
Yorodumi- PDB-9t5t: Chlorophyll f-containing dimeric far-red Photosystem II from Chro... -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 9t5t | ||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Title | Chlorophyll f-containing dimeric far-red Photosystem II from Chroococcidiopsis thermalis PCC 7203 | ||||||||||||||||||||||||||||||||||||
Components |
| ||||||||||||||||||||||||||||||||||||
Keywords | ELECTRON TRANSPORT / Chlorophyll f / photosystem II / FaRLiP | ||||||||||||||||||||||||||||||||||||
| Function / homology | Function and homology informationphotosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / extrinsic component of membrane / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / phosphate ion binding / photosynthesis, light reaction / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||||||||||||||||||||||||||
| Biological species | Chroococcidiopsis thermalis PCC 7203 (bacteria) | ||||||||||||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.17 Å | ||||||||||||||||||||||||||||||||||||
Authors | Leong, H.F. / Consoli, G. / Murray, J.W. / Fantuzzi, A. / Rutherford, A.W. | ||||||||||||||||||||||||||||||||||||
| Funding support | United Kingdom, European Union, 11items
| ||||||||||||||||||||||||||||||||||||
Citation | Journal: Nat Commun / Year: 2026Title: Mapping the absorption landscape of far-red Photosystem II Authors: Leong, H.F. / Consoli, G. / Davis, G.A. / Hancox-Lachman, B. / Renard, K. / Tufail, F. / Lee, L.E. / Gautier, L. / Murray, J.W. / Fantuzzi, A. / Rutherford, A.W. | ||||||||||||||||||||||||||||||||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 9t5t.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb9t5t.ent.gz | 1.1 MB | Display | PDB format |
| PDBx/mmJSON format | 9t5t.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/9t5t ftp://data.pdbj.org/pub/pdb/validation_reports/t5/9t5t | HTTPS FTP |
|---|
-Related structure data
| Related structure data | ![]() 55593MC ![]() 9t5uC C: citing same article ( M: map data used to model this data |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
-
Assembly
| Deposited unit | ![]()
|
|---|---|
| 1 |
|
-
Components
-Photosystem II ... , 18 types, 36 molecules AaBbCcDdHhIiJjKkLlMmOoRrTtUuVv...
| #1: Protein | Mass: 40732.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TVY6, photosystem II #2: Protein | Mass: 57614.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TWK6 #3: Protein | Mass: 50827.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TVH2 #4: Protein | Mass: 39825.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TX47, photosystem II #8: Protein | Mass: 7834.357 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TVZ5 #9: Protein/peptide | Mass: 4377.158 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TRV7 #10: Protein/peptide | Mass: 4015.678 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TZ53 #11: Protein | Mass: 6690.924 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TSZ1 #12: Protein/peptide | Mass: 4762.552 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TXA1 #13: Protein/peptide | Mass: 4156.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9U8J8 #14: Protein | Mass: 29794.619 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TX16 #15: Protein/peptide | Mass: 4505.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9U462 #16: Protein/peptide | Mass: 3654.408 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9U9A4 #17: Protein | Mass: 16995.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9U3E1 #18: Protein | Mass: 17602.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TVF4 #19: Protein/peptide | Mass: 4326.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9U6Z0 #20: Protein/peptide | Mass: 4660.479 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TVN1 #21: Protein | Mass: 6890.349 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9U4H5 |
|---|
-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
| #5: Protein | Mass: 9465.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TZN4 #6: Protein/peptide | Mass: 5065.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TYK3 |
|---|
-Protein/peptide , 1 types, 2 molecules Gg
| #7: Protein/peptide | Mass: 5323.152 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Chroococcidiopsis thermalis PCC 7203 (bacteria)References: UniProt: K9TX50 |
|---|
-Sugars , 2 types, 26 molecules 


| #32: Sugar | ChemComp-LMT / #35: Sugar | ChemComp-DGD / |
|---|
-Non-polymers , 16 types, 818 molecules 




























| #22: Chemical | | #23: Chemical | #24: Chemical | ChemComp-CL / #25: Chemical | ChemComp-CLA / #26: Chemical | #27: Chemical | ChemComp-PHO / #28: Chemical | ChemComp-BCR / #29: Chemical | ChemComp-SQD / #30: Chemical | ChemComp-PL9 / #31: Chemical | ChemComp-LMG / #33: Chemical | ChemComp-LHG / #34: Chemical | ChemComp-F6C / #36: Chemical | #37: Chemical | #38: Chemical | #39: Water | ChemComp-HOH / | |
|---|
-Details
| Has ligand of interest | Y |
|---|---|
| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
|---|---|
| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
| Component | Name: Dimeric far-red Photosystem II / Type: COMPLEX Details: Chlorophyll f-containing dimeric far-red Photosystem II from Chroococcidiopsis thermalis PCC 7203 Entity ID: #1-#21 / Source: NATURAL |
|---|---|
| Molecular weight | Value: 0.69 MDa / Experimental value: NO |
| Source (natural) | Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria) |
| Buffer solution | pH: 6.5 Details: 50 mM MES, 1 M betaine monohydrate, 20 mM CaCl2, 5 mM MgCl2 and 10% (v/v) glycerol, pH 6.8 adjusted with NaOH |
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-
Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
|---|---|
| Microscopy | Model: TFS KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
| Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
| Image scans | Width: 4096 / Height: 4096 |
-
Processing
| EM software |
| ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
| Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
| 3D reconstruction | Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49763 / Symmetry type: POINT | ||||||||||||||||||||||||
| Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
| Displacement parameters | Biso mean: 88.53 Å2 | ||||||||||||||||||||||||
| Refine LS restraints |
|
Movie
Controller
About Yorodumi



Chroococcidiopsis thermalis PCC 7203 (bacteria)
United Kingdom, European Union, 11items
Citation


PDBj



















FIELD EMISSION GUN