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Yorodumi- PDB-7dwq: Photosystem I from a chlorophyll d-containing cyanobacterium Acar... -
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-Basic information
Entry | Database: PDB / ID: 7dwq | ||||||
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Title | Photosystem I from a chlorophyll d-containing cyanobacterium Acaryochloris marina | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem I / reaction center / cryo-EM / cyanobacteria | ||||||
Function / homology | Function and homology information photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem I / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Acaryochloris marina MBIC11017 (bacteria) Acaryochloris marinan MBIC11017 (bacteria) Acaryochloris marina MBIC 11017 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Chen, J.H. / Zhang, X. / Shen, J.R. | ||||||
Citation | Journal: J Integr Plant Biol / Year: 2021 Title: A unique photosystem I reaction center from a chlorophyll d-containing cyanobacterium Acaryochloris marina. Authors: Caihuang Xu / Qingjun Zhu / Jing-Hua Chen / Liangliang Shen / Xiaohan Yi / Zihui Huang / Wenda Wang / Min Chen / Tingyun Kuang / Jian-Ren Shen / Xing Zhang / Guangye Han / Abstract: Photosystem I (PSI) is a large protein supercomplex that catalyzes the light-dependent oxidation of plastocyanin (or cytochrome c ) and the reduction of ferredoxin. This catalytic reaction is ...Photosystem I (PSI) is a large protein supercomplex that catalyzes the light-dependent oxidation of plastocyanin (or cytochrome c ) and the reduction of ferredoxin. This catalytic reaction is realized by a transmembrane electron transfer chain consisting of primary electron donor (a special chlorophyll (Chl) pair) and electron acceptors A , A , and three Fe S clusters, F , F , and F . Here we report the PSI structure from a Chl d-dominated cyanobacterium Acaryochloris marina at 3.3 Å resolution obtained by single-particle cryo-electron microscopy. The A. marina PSI exists as a trimer with three identical monomers. Surprisingly, the structure reveals a unique composition of electron transfer chain in which the primary electron acceptor A is composed of two pheophytin a rather than Chl a found in any other well-known PSI structures. A novel subunit Psa27 is observed in the A. marina PSI structure. In addition, 77 Chls, 13 α-carotenes, two phylloquinones, three Fe-S clusters, two phosphatidyl glycerols, and one monogalactosyl-diglyceride were identified in each PSI monomer. Our results provide a structural basis for deciphering the mechanism of photosynthesis in a PSI complex with Chl d as the dominating pigments and absorbing far-red light. | ||||||
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 | 7dwq.cif.gz | 446.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dwq.ent.gz | 394.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dwq_validation.pdf.gz | 5.8 MB | Display | wwPDB validaton report |
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Full document | 7dwq_full_validation.pdf.gz | 6.2 MB | Display | |
Data in XML | 7dwq_validation.xml.gz | 106.7 KB | Display | |
Data in CIF | 7dwq_validation.cif.gz | 139.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/7dwq ftp://data.pdbj.org/pub/pdb/validation_reports/dw/7dwq | HTTPS FTP |
-Related structure data
Related structure data | 30882MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Photosystem I protein ... , 4 types, 4 molecules DFLW
#1: Protein | Mass: 15114.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 / References: UniProt: B0C8F1 |
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#6: Protein | Mass: 17844.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 / References: UniProt: B0C7S7 |
#8: Protein | Mass: 15349.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acaryochloris marina MBIC 11017 (bacteria) Strain: MBIC 11017 / References: UniProt: B0C7S4 |
#10: Protein/peptide | Mass: 3648.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 |
-Photosystem I P740 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#2: Protein | Mass: 83470.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 / References: UniProt: B0C474, photosystem I |
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#3: Protein | Mass: 82210.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 / References: UniProt: B0C475, photosystem I |
-Protein , 1 types, 1 molecules C
#4: Protein | Mass: 8825.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acaryochloris marinan MBIC11017 (bacteria) Strain: MBIC 11017 / References: UniProt: B0CB42, photosystem I |
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-Photosystem I reaction center subunit ... , 3 types, 3 molecules EJM
#5: Protein | Mass: 9560.822 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 / References: UniProt: B0C5D5 |
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#7: Protein | Mass: 5900.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acaryochloris marina MBIC 11017 (bacteria) Strain: MBIC 11017 / References: UniProt: B0C7S6 |
#9: Protein/peptide | Mass: 3190.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 |
-Non-polymers , 8 types, 100 molecules
#11: Chemical | ChemComp-CL7 / #12: Chemical | #13: Chemical | #14: Chemical | #15: Chemical | ChemComp-G9R / | #16: Chemical | #17: Chemical | ChemComp-8CT / ( #18: Chemical | ChemComp-LMG / | |
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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: Photosystem I from a chlorophyll d-containing cyanobacterium Acaryochloris marina Type: COMPLEX / Entity ID: #1-#10 / 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 |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-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 / Nominal magnification: 22500 X / Calibrated magnification: 38244 X / Nominal defocus max: 3000 nm / Nominal defocus min: 2500 nm / Calibrated defocus min: 2500 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 47 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 4 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1523356 / Details: raw particles | ||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 240880 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
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