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Yorodumi- PDB-8wql: In situ PBS-PSII supercomplex from cyanobacterial Spirulina platensis -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wql | ||||||
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Title | In situ PBS-PSII supercomplex from cyanobacterial Spirulina platensis | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / complex | ||||||
Function / homology | Function and homology information phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||
Biological species | Arthrospira sp. FACHB-439 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | You, X. / Zhang, X. / Xiao, Y.N. / Sun, S. / Sui, S.F. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of in situ PBS-PSII supercomplex at 3.5 Angstroms resolution. Authors: You, X. / Zhang, X. / Xiao, Y.N. / Sun, S. / Sui, S.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wql.cif.gz | 12 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8wql.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8wql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wql_validation.pdf.gz | 47.7 MB | Display | wwPDB validaton report |
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Full document | 8wql_full_validation.pdf.gz | 45.5 MB | Display | |
Data in XML | 8wql_validation.xml.gz | 2.1 MB | Display | |
Data in CIF | 8wql_validation.cif.gz | 2.8 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/8wql ftp://data.pdbj.org/pub/pdb/validation_reports/wq/8wql | HTTPS FTP |
-Related structure data
Related structure data | 37749MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 9 types, 192 molecules BABCBHBIBJB2B3B5B6B7B8B9BBCBB4C4UBNFNKb4U4bB3F2G8G3K2L8LQDQE...
#1: Protein | Mass: 29443.213 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria) #2: Protein | Mass: 102100.633 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria) #5: Protein | Mass: 7775.107 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcC / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZBQ2 #19: Protein | Mass: 18641.410 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbQ / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZQ11 #23: Protein | Mass: 10733.153 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria) #28: Protein | Mass: 15788.175 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZJ52 #30: Protein | Mass: 18022.709 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcD / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZH43 #31: Protein | Mass: 17616.848 Da / Num. of mol.: 72 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: cpcA / Production host: Arthrospira sp. FACHB-439 (bacteria) #32: Protein | Mass: 18062.441 Da / Num. of mol.: 72 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: cpcB / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A9UKJ0 |
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-Allophycocyanin ... , 3 types, 136 molecules OBQBSBVBXBZBJFLFXFZFAGGGIGKGNGPGRGTGJKLKXKZKALGLILKLNLPLRLTL...
#3: Protein | Mass: 17409.799 Da / Num. of mol.: 64 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcA / Production host: Arthrospira sp. FACHB-439 (bacteria) #4: Protein | Mass: 17345.748 Da / Num. of mol.: 68 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcB / Production host: Arthrospira sp. FACHB-439 (bacteria) #29: Protein | Mass: 18446.771 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: apcF / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZN25 |
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-Photosystem II ... , 17 types, 102 molecules ADAEA1a1aDaEBDBEB1b1bDbECDCEC1c1cDcEDDDED1d1dDdEHDHEH1h1hDhE...
#6: Protein | Mass: 39675.184 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbA1 / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4ENJ6, photosystem II #7: Protein | Mass: 56256.766 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbB / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EP29 #8: Protein | Mass: 51545.973 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbC / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EL13 #9: Protein | Mass: 39521.270 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbD1, psbD / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EL11, photosystem II #12: Protein | Mass: 7636.935 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbH / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZFR1 #13: Protein/peptide | Mass: 4414.285 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbI / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EN47 #14: Protein/peptide | Mass: 3914.632 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbJ / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZEX7 #15: Protein/peptide | Mass: 4979.012 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbK / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EP73 #16: Protein/peptide | Mass: 4581.344 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbL / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZAC5 #17: Protein/peptide | Mass: 4128.829 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbM / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZMZ9 #18: Protein | Mass: 30064.770 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbO / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZRB6 #20: Protein/peptide | Mass: 4189.124 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbY / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZG21 #22: Protein/peptide | Mass: 3439.182 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbTc, psbT / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EP38 #24: Protein | Mass: 18165.770 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbV1, psbV / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4ELM7 #25: Protein/peptide | Mass: 5427.645 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbX / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZPA1 #26: Protein/peptide | Mass: 4692.648 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psb30 / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZL09 #27: Protein | Mass: 6848.350 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbZ / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZFP8 |
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-Cytochrome b559 subunit ... , 2 types, 12 molecules EDEEE1e1eDeEFDFEF1f1fDfE
#10: Protein | Mass: 9344.573 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbE / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W4EIR1 #11: Protein/peptide | Mass: 4994.852 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Gene: psbF / Production host: Arthrospira sp. FACHB-439 (bacteria) / References: UniProt: A0A9W3ZAF8 |
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-Protein/peptide , 1 types, 3 molecules SDSES1
#21: Protein/peptide | Mass: 4017.944 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrospira sp. FACHB-439 (bacteria) / Production host: Arthrospira sp. FACHB-439 (bacteria) |
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-Sugars , 2 types, 78 molecules
#40: Sugar | ChemComp-LMT / #44: Sugar | ChemComp-DGD / |
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-Non-polymers , 14 types, 804 molecules
#33: Chemical | ChemComp-CYC / #34: Chemical | ChemComp-OEX / #35: Chemical | ChemComp-CL / #36: Chemical | ChemComp-CLA / #37: Chemical | ChemComp-PL9 / #38: Chemical | ChemComp-SQD / #39: Chemical | ChemComp-LMG / #41: Chemical | ChemComp-BCT / #42: Chemical | ChemComp-LHG / #43: Chemical | ChemComp-BCR / #45: Chemical | ChemComp-PHO / #46: Chemical | ChemComp-FE2 / #47: Chemical | ChemComp-HEM / #48: Chemical | ChemComp-CA / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: In situ PBS-PSII supercomplex / Type: CELL / Entity ID: #1-#32 / Source: NATURAL |
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Source (natural) | Organism: Arthrospira platensis (bacteria) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 6000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 6000 nm |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168000 / Symmetry type: POINT |