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Yorodumi- PDB-7coy: Structure of the far-red light utilizing photosystem I of Acaryoc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7coy | ||||||||||||||||||
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Title | Structure of the far-red light utilizing photosystem I of Acaryochloris marina | ||||||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem I / Acaryochloris marina / Light-harvesting / Chlorophyll d | ||||||||||||||||||
Function / homology | Function and homology information 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 / electron transfer activity ...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 / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Acaryochloris marina MBIC11017 (bacteria) Acaryochloris marina MBIC110017 (bacteria) Acaryochloris marina MBIC 11017 (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||||||||||||||
Authors | Kawakami, K. / Yonekura, K. / Hamaguchi, T. / Kashino, Y. / Shinzawa-Itoh, K. / Inoue-Kashino, N. / Itoh, S. / Ifuku, K. / Yamashita, E. | ||||||||||||||||||
Funding support | Japan, 5items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structure of the far-red light utilizing photosystem I of Acaryochloris marina. Authors: Tasuku Hamaguchi / Keisuke Kawakami / Kyoko Shinzawa-Itoh / Natsuko Inoue-Kashino / Shigeru Itoh / Kentaro Ifuku / Eiki Yamashita / Kou Maeda / Koji Yonekura / Yasuhiro Kashino / Abstract: Acaryochloris marina is one of the cyanobacterial species that can use far-red light to drive photochemical reactions for oxygenic photosynthesis. Here, we report the structure of A. marina ...Acaryochloris marina is one of the cyanobacterial species that can use far-red light to drive photochemical reactions for oxygenic photosynthesis. Here, we report the structure of A. marina photosystem I (PSI) reaction center, determined by cryo-electron microscopy at 2.58 Å resolution. The structure reveals an arrangement of electron carriers and light-harvesting pigments distinct from other type I reaction centers. The paired chlorophyll, or special pair (also referred to as P740 in this case), is a dimer of chlorophyll d and its epimer chlorophyll d'. The primary electron acceptor is pheophytin a, a metal-less chlorin. We show the architecture of this PSI reaction center is composed of 11 subunits and we identify key components that help explain how the low energy yield from far-red light is efficiently utilized for driving oxygenic photosynthesis. | ||||||||||||||||||
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 | 7coy.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7coy.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7coy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7coy_validation.pdf.gz | 13.6 MB | Display | wwPDB validaton report |
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Full document | 7coy_full_validation.pdf.gz | 14.4 MB | Display | |
Data in XML | 7coy_validation.xml.gz | 275.5 KB | Display | |
Data in CIF | 7coy_validation.cif.gz | 363.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/7coy ftp://data.pdbj.org/pub/pdb/validation_reports/co/7coy | HTTPS FTP |
-Related structure data
Related structure data | 30420MC 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 P700 chlorophyll a apoprotein ... , 2 types, 6 molecules aAbAcAaBbBcB
#1: Protein | Mass: 83470.539 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 / References: UniProt: B0C474, photosystem I #2: Protein | Mass: 82210.555 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Acaryochloris marina MBIC110017 (bacteria) Strain: MBIC 11017 / References: UniProt: B0C475, photosystem I |
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-Protein , 1 types, 3 molecules aCbCcC
#3: Protein | Mass: 8825.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Acaryochloris marina MBIC110017 (bacteria) Strain: MBIC 11017 / References: UniProt: B0CB42, photosystem I |
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-Photosystem I protein ... , 5 types, 15 molecules aDbDcDaFbFcFaIbIcIaLbLcLaMbMcM
#4: Protein | Mass: 15114.146 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Acaryochloris marina MBIC110017 (bacteria) Strain: MBIC 11017 / References: UniProt: B0C8F1 #6: Protein | Mass: 17844.621 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Acaryochloris marina MBIC110017 (bacteria) Strain: MBIC 11017 / References: UniProt: B0C7S7 #7: Protein/peptide | Mass: 3648.337 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 #10: Protein | Mass: 15349.588 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Acaryochloris marina MBIC 11017 (bacteria) Strain: MBIC 11017 / References: UniProt: B0C7S4 #11: Protein/peptide | Mass: 3190.899 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina MBIC11017 (bacteria) / Strain: MBIC 11017 |
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-Photosystem I reaction center subunit ... , 3 types, 9 molecules aEbEcEaJbJcJaKbKcK
#5: Protein | Mass: 9560.822 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Acaryochloris marina MBIC110017 (bacteria) Strain: MBIC 11017 / References: UniProt: B0C5D5 #8: Protein | Mass: 5900.939 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Acaryochloris marina MBIC110017 (bacteria) Strain: MBIC 11017 / References: UniProt: B0C7S6 #9: Protein | Mass: 9289.071 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Acaryochloris marina MBIC 11017 (bacteria) Strain: MBIC 11017 / References: UniProt: B0CA71 |
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-Non-polymers , 9 types, 363 molecules
#12: Chemical | #13: Chemical | ChemComp-PHO / #14: Chemical | ChemComp-CL7 / #15: Chemical | ChemComp-UNL / Num. of mol.: 36 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION #16: Chemical | ChemComp-LHG / #17: Chemical | ChemComp-PQN / #18: Chemical | ChemComp-SF4 / #19: Chemical | #20: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Nonpolymer details | Authors state that Photosystem I from Acaryochloris marina contains alfa-carotene instead of beta- ...Authors state that Photosystem I from Acaryochloris marina contains alfa-carotene instead of beta-carotene. The alfa-carotene molecule possesses two rings (known as beta- and epsilon-rings) at each end, while the beta-carotene possesses two beta-rings. From the cryo-EM density map, they could not distinguish the difference between beta- and epsilon-ring, because the only difference between beta- and epsilon-ring is the arrangement of the hydrogen atom. Therefore such unclear molecules have been assigned to UNL. |
-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 complex from Acaryochloris marina / Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL |
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Source (natural) | Organism: Acaryochloris marina (bacteria) |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 85.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86419 / Symmetry type: POINT |
Refinement | Highest resolution: 2.5 Å |