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Open data
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Basic information
Entry | Database: PDB / ID: 8wmv | |||||||||
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Title | The structure of PSI-14CAC complex at stationary growth phase | |||||||||
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![]() | PHOTOSYNTHESIS / chlorophyll c / alloxanthin / growth phase | |||||||||
Function / homology | ![]() 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 / oxidoreductase activity / electron transfer 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 / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å | |||||||||
![]() | Zhang, S.M. / Si, L. / Li, M. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 18.4 MB | Display | ![]() |
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Full document | ![]() | 19.9 MB | Display | |
Data in XML | ![]() | 349.9 KB | Display | |
Data in CIF | ![]() | 403.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 37659MC ![]() 8wm6C ![]() 8wmjC ![]() 8wmwC ![]() 8wnwC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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) ![]() |
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#2: Protein | Mass: 82069.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 16 types, 18 molecules COscabhmfjelkidgRn
#3: Protein | Mass: 8759.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||||
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#11: Protein | Mass: 15133.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||||
#13: Protein | Mass: 27966.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||||
#14: Protein | Mass: 23781.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||||
#15: Protein | Mass: 23330.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||||
#16: Protein | Mass: 23503.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||||
#17: Protein | Mass: 23132.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||||||||||
#18: Protein | Mass: 22272.936 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() #19: Protein | | Mass: 21787.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #20: Protein | | Mass: 25908.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #21: Protein | | Mass: 25588.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #22: Protein | | Mass: 23078.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #23: Protein | | Mass: 22391.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #24: Protein | | Mass: 26979.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #25: Protein | | Mass: 13318.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #26: Protein | | Mass: 22876.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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#5: Protein | Mass: 7309.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 20817.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein/peptide | Mass: 3927.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein/peptide | Mass: 4974.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#9: Protein | Mass: 16475.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: Protein/peptide | Mass: 3318.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 8715.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Sugars , 3 types, 6 molecules ![](data/chem/img/LMT.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/LMU.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/LMU.gif)
#31: Sugar | ChemComp-LMT / #33: Sugar | ChemComp-DGD / | #38: Sugar | ChemComp-LMU / | |
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-Non-polymers , 10 types, 538 molecules ![](data/chem/img/CLA.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/II0.gif)
![](data/chem/img/IHT.gif)
![](data/chem/img/KC2.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/II0.gif)
![](data/chem/img/IHT.gif)
![](data/chem/img/KC2.gif)
![](data/chem/img/HOH.gif)
#27: Chemical | ChemComp-CLA / #28: Chemical | #29: Chemical | ChemComp-LHG / #30: Chemical | ChemComp-WVN / Mass: 536.873 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION #32: Chemical | #34: Chemical | ChemComp-LMG / #35: Chemical | ChemComp-II0 / ( #36: Chemical | ChemComp-IHT / ( #37: Chemical | ChemComp-KC2 / #39: 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 |
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Sample preparation
Component | Name: PSI-14CAC(L-phase) / Type: COMPLEX / Entity ID: #1-#26 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42423 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.22 Å2 | ||||||||||||||||||||||||
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