+Open data
-Basic information
Entry | Database: PDB / ID: 7ymi | ||||||||||||
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Title | PSII-Pcb Dimer of Acaryochloris Marina | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem II / Pcb | ||||||||||||
Function / homology | Function and homology information photosystem / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthesis, light reaction ...photosystem / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthesis, light reaction / phosphate ion binding / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Acaryochloris marina MBIC11017 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Shen, L.L. / Gao, Y.Z. / Wang, W.D. / Zhang, X. / Shen, J.R. / Wang, P.Y. / Han, G.Y. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Sci Adv / Year: 2024 Title: Structure of a unique PSII-Pcb tetrameric megacomplex in a chlorophyll -containing cyanobacterium. Authors: Liangliang Shen / Yuanzhu Gao / Kailu Tang / Ruxi Qi / Lutang Fu / Jing-Hua Chen / Wenda Wang / Xiaomin Ma / Peiyao Li / Min Chen / Tingyun Kuang / Xing Zhang / Jian-Ren Shen / Peiyi Wang / Guangye Han / Abstract: is a unique cyanobacterium using chlorophyll (Chl ) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of associates with a number of prochlorophyte Chl- ... is a unique cyanobacterium using chlorophyll (Chl ) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of associates with a number of prochlorophyte Chl-binding (Pcb) proteins to act as the light-harvesting system. We report here the cryo-electron microscopic structure of a PSII-Pcb megacomplex from at a 3.6-angstrom overall resolution and a 3.3-angstrom local resolution. The megacomplex is organized as a tetramer consisting of two PSII core dimers flanked by sixteen symmetrically related Pcb proteins, with a total molecular weight of 1.9 megadaltons. The structure reveals the detailed organization of PSII core consisting of 15 known protein subunits and an unknown subunit, the assembly of 4 Pcb antennas within each PSII monomer, and possible pathways of energy transfer within the megacomplex, providing deep insights into energy transfer and dissipation mechanisms within the PSII-Pcb megacomplex involved in far-red light utilization. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ymi.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ymi.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 7ymi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ymi_validation.pdf.gz | 15.3 MB | Display | wwPDB validaton report |
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Full document | 7ymi_full_validation.pdf.gz | 16.2 MB | Display | |
Data in XML | 7ymi_validation.xml.gz | 335.1 KB | Display | |
Data in CIF | 7ymi_validation.cif.gz | 421.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/7ymi ftp://data.pdbj.org/pub/pdb/validation_reports/ym/7ymi | HTTPS FTP |
-Related structure data
Related structure data | 33929MC 7ymmC 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
-Photosystem II ... , 14 types, 28 molecules AaBbCcDdFfHhIiKkLlMmTtXxYyZz
#1: Protein | Mass: 39695.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: A5A8K9, photosystem II #2: Protein | Mass: 56518.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0CFM2 #3: Protein | Mass: 53978.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C1V7 #4: Protein | Mass: 39291.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C1V6, photosystem II #6: Protein | Mass: 11277.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C2V2 #7: Protein | Mass: 7683.901 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0CDZ2 #8: Protein/peptide | Mass: 3948.692 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C5R5 #9: Protein/peptide | Mass: 4939.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6Z7 #10: Protein/peptide | Mass: 4254.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6T1 #11: Protein/peptide | Mass: 3614.302 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0CFM0 #12: Protein/peptide | Mass: 5442.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C605 #13: Protein/peptide | Mass: 4443.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0BYW9 #14: Protein/peptide | Mass: 4015.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) #15: Protein | Mass: 6395.632 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C0S7 |
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-High light inducible ... , 4 types, 8 molecules 26153748
#16: Protein | Mass: 38753.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C3E5 #18: Protein | Mass: 38612.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C576 #19: Protein | Mass: 38707.781 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6I0 #20: Protein | Mass: 37967.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C3E6 |
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-Protein / Protein/peptide / Sugars , 3 types, 8 molecules EeGg
#17: Protein/peptide | Mass: 3507.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) #27: Sugar | ChemComp-DGD / #5: Protein | Mass: 9495.788 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / References: UniProt: B0C6T2 |
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-Non-polymers , 11 types, 308 molecules
#21: Chemical | ChemComp-CL7 / #22: Chemical | ChemComp-PHO / #23: Chemical | ChemComp-8CT / ( #24: Chemical | ChemComp-SQD / #25: Chemical | ChemComp-LHG / #26: Chemical | ChemComp-LMG / #28: Chemical | #29: Chemical | #30: Chemical | #31: Chemical | #32: Chemical | ChemComp-ZEX / ( |
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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: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: PSII-Pcb Dimer of Acaryochloris Marina / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL |
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Source (natural) | Organism: Acaryochloris marina MBIC11017 (bacteria) |
Buffer solution | pH: 6.5 |
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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132346 / Symmetry type: POINT |