+Open data
-Basic information
Entry | Database: PDB / ID: 8wmj | |||||||||
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Title | structure of PSI-11CAC complex at Logrithmic growth phase | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / alloxanthin / chlorophyll c / PsaQ | |||||||||
Function / homology | Function and homology information photosystem I reaction center / photosystem I / photosystem I / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosystem I / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Rhodomonas salina (eukaryote) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Zhang, S.M. / Si, L. / Li, M. | |||||||||
Funding support | China, 2items
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Citation | Journal: Commun Biol / Year: 2024 Title: Growth phase-dependent reorganization of cryptophyte photosystem I antennae. Authors: Shumeng Zhang / Long Si / Xiaodong Su / Xuelin Zhao / Xiaomin An / Mei Li / Abstract: Photosynthetic cryptophytes are eukaryotic algae that utilize membrane-embedded chlorophyll a/c binding proteins (CACs) and lumen-localized phycobiliproteins (PBPs) as their light-harvesting antennae. ...Photosynthetic cryptophytes are eukaryotic algae that utilize membrane-embedded chlorophyll a/c binding proteins (CACs) and lumen-localized phycobiliproteins (PBPs) as their light-harvesting antennae. Cryptophytes go through logarithmic and stationary growth phases, and may adjust their light-harvesting capability according to their particular growth state. How cryptophytes change the type/arrangement of the photosynthetic antenna proteins to regulate their light-harvesting remains unknown. Here we solve four structures of cryptophyte photosystem I (PSI) bound with CACs that show the rearrangement of CACs at different growth phases. We identify a cryptophyte-unique protein, PsaQ, which harbors two chlorophyll molecules. PsaQ specifically binds to the lumenal region of PSI during logarithmic growth phase and may assist the association of PBPs with photosystems and energy transfer from PBPs to photosystems. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wmj.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8wmj.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 8wmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wmj_validation.pdf.gz | 15.9 MB | Display | wwPDB validaton report |
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Full document | 8wmj_full_validation.pdf.gz | 17 MB | Display | |
Data in XML | 8wmj_validation.xml.gz | 300.5 KB | Display | |
Data in CIF | 8wmj_validation.cif.gz | 353.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/8wmj ftp://data.pdbj.org/pub/pdb/validation_reports/wm/8wmj | HTTPS FTP |
-Related structure data
Related structure data | 37654MC 8wm6C 8wmvC 8wmwC 8wnwC 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 I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 83431.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVZ7 |
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#2: Protein | Mass: 82069.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVZ6 |
-Protein , 14 types, 15 molecules CscabhmjlkidRnQ
#3: Protein | Mass: 8759.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVS8 | ||||||||||||||
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#12: Protein | Mass: 27966.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) | ||||||||||||||
#13: Protein | Mass: 23781.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) | ||||||||||||||
#14: Protein | Mass: 23330.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) | ||||||||||||||
#15: Protein | Mass: 23503.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) | ||||||||||||||
#16: Protein | Mass: 23132.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) | ||||||||||||||
#17: Protein | Mass: 22272.936 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) #18: Protein | | Mass: 25908.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) #19: Protein | | Mass: 25588.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) #20: Protein | | Mass: 23078.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) #21: Protein | | Mass: 22391.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) #22: Protein | | Mass: 13318.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) #23: Protein | | Mass: 22876.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) #24: Protein | | Mass: 23834.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) |
-Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFIJLMK
#4: Protein | Mass: 15585.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVZ1 |
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#5: Protein | Mass: 7309.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MW36 |
#6: Protein | Mass: 20817.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVU7 |
#7: Protein/peptide | Mass: 3927.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVV1 |
#8: Protein/peptide | Mass: 4974.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVU6 |
#9: Protein | Mass: 16475.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVV8 |
#10: Protein/peptide | Mass: 3318.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVT4 |
#11: Protein | Mass: 8715.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas salina (eukaryote) / References: UniProt: A6MVS9 |
-Sugars , 3 types, 6 molecules
#29: Sugar | ChemComp-LMT / #31: Sugar | ChemComp-DGD / | #36: Sugar | ChemComp-LMU / | |
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-Non-polymers , 10 types, 476 molecules
#25: Chemical | ChemComp-CLA / #26: Chemical | #27: Chemical | ChemComp-LHG / #28: Chemical | ChemComp-WVN / Mass: 536.873 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION #30: Chemical | #32: Chemical | ChemComp-II0 / ( #33: Chemical | ChemComp-LMG / #34: Chemical | ChemComp-KC2 / #35: Chemical | ChemComp-IHT / ( #37: Water | ChemComp-HOH / | |
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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: PSI-CAC / Type: COMPLEX / Entity ID: #1-#16, #18-#20, #17, #21-#24 / Source: NATURAL |
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Source (natural) | Organism: Rhodomonas salina (eukaryote) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41093 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.67 Å2 | ||||||||||||||||||||||||
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