+Open data
-Basic information
Entry | Database: PDB / ID: 6zzx | |||||||||
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Title | Structure of low-light grown Chlorella ohadii Photosystem I | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / photosystem I / light stress | |||||||||
Function / homology | Function and homology information malate transport / photosynthesis, light harvesting / glutathione-disulfide reductase (NADPH) activity / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / photosystem II ...malate transport / photosynthesis, light harvesting / glutathione-disulfide reductase (NADPH) activity / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / photosystem II / chloroplast thylakoid membrane / acyltransferase activity, transferring groups other than amino-acyl groups / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / chlorophyll binding / response to light stimulus / photosynthesis / glutathione metabolic process / cell redox homeostasis / monooxygenase activity / chloroplast / membrane => GO:0016020 / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / cellular response to oxidative stress / electron transfer activity / cytoskeleton / oxidoreductase activity / protein kinase activity / iron ion binding / heme binding / magnesium ion binding / mitochondrion / ATP binding / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Chlorella ohadii (plant) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Caspy, I. / Nelson, N. / Nechushtai, R. / Neumann, E. / Shkolnisky, Y. | |||||||||
Funding support | Israel, 2items
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Citation | Journal: Nat Plants / Year: 2021 Title: Cryo-EM photosystem I structure reveals adaptation mechanisms to extreme high light in Chlorella ohadii. Authors: Ido Caspy / Ehud Neumann / Maria Fadeeva / Varda Liveanu / Anton Savitsky / Anna Frank / Yael Levi Kalisman / Yoel Shkolnisky / Omer Murik / Haim Treves / Volker Hartmann / Marc M Nowaczyk / ...Authors: Ido Caspy / Ehud Neumann / Maria Fadeeva / Varda Liveanu / Anton Savitsky / Anna Frank / Yael Levi Kalisman / Yoel Shkolnisky / Omer Murik / Haim Treves / Volker Hartmann / Marc M Nowaczyk / Wolfgang Schuhmann / Matthias Rögner / Itamar Willner / Aaron Kaplan / Gadi Schuster / Nathan Nelson / Wolfgang Lubitz / Rachel Nechushtai / Abstract: Photosynthesis in deserts is challenging since it requires fast adaptation to rapid night-to-day changes, that is, from dawn's low light (LL) to extreme high light (HL) intensities during the daytime. ...Photosynthesis in deserts is challenging since it requires fast adaptation to rapid night-to-day changes, that is, from dawn's low light (LL) to extreme high light (HL) intensities during the daytime. To understand these adaptation mechanisms, we purified photosystem I (PSI) from Chlorella ohadii, a green alga that was isolated from a desert soil crust, and identified the essential functional and structural changes that enable the photosystem to perform photosynthesis under extreme high light conditions. The cryo-electron microscopy structures of PSI from cells grown under low light (PSI) and high light (PSI), obtained at 2.70 and 2.71 Å, respectively, show that part of light-harvesting antenna complex I (LHCI) and the core complex subunit (PsaO) are eliminated from PSI to minimize the photodamage. An additional change is in the pigment composition and their number in LHCI; about 50% of chlorophyll b is replaced by chlorophyll a. This leads to higher electron transfer rates in PSI and might enable C. ohadii PSI to act as a natural photosynthesiser in photobiocatalytic systems. PSI or PSI were attached to an electrode and their induced photocurrent was determined. To obtain photocurrents comparable with PSI, 25 times the amount of PSI was required, demonstrating the high efficiency of PSI. Hence, we suggest that C. ohadii PSI is an ideal candidate for the design of desert artificial photobiocatalytic systems. | |||||||||
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 | 6zzx.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6zzx.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6zzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zzx_validation.pdf.gz | 17.6 MB | Display | wwPDB validaton report |
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Full document | 6zzx_full_validation.pdf.gz | 19 MB | Display | |
Data in XML | 6zzx_validation.xml.gz | 363.3 KB | Display | |
Data in CIF | 6zzx_validation.cif.gz | 427.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/6zzx ftp://data.pdbj.org/pub/pdb/validation_reports/zz/6zzx | HTTPS FTP |
-Related structure data
Related structure data | 11588MC 6zzyC 7a4pC 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 ... , 13 types, 13 molecules ABCDEGHJKLMIO
#1: Protein | Mass: 82125.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SY74, photosystem I |
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#2: Protein | Mass: 81544.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SUA3, photosystem I |
#3: Protein | Mass: 8723.009 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SKM2, photosystem I |
#4: Protein | Mass: 15958.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TKF8 |
#5: Protein | Mass: 7194.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6U4S6 |
#7: Protein | Mass: 10326.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TZI8 |
#8: Protein | Mass: 10319.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TPU7 |
#9: Protein/peptide | Mass: 4475.292 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SUD1 |
#10: Protein | Mass: 8725.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6U0J1 |
#11: Protein | Mass: 16501.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TC44 |
#12: Protein/peptide | Mass: 3376.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SU98 |
#13: Protein/peptide | Mass: 3856.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: W8SIP9 |
#14: Protein | Mass: 9547.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6THB2 |
-Protein , 4 types, 4 molecules F347
#6: Protein | Mass: 18069.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TPV8 |
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#16: Protein | Mass: 26163.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TMT4 |
#17: Protein | Mass: 23010.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) |
#20: Protein | Mass: 24016.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) |
-Chlorophyll a-b binding protein, ... , 6 types, 7 molecules 1a56829
#15: Protein | Mass: 19933.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TT36 #18: Protein | | Mass: 25371.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6U4K1 #19: Protein | | Mass: 25316.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TPR7 #21: Protein | | Mass: 23612.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TZ50 #22: Protein | | Mass: 23618.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TMX4 #23: Protein | | Mass: 19911.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorella ohadii (plant) / References: UniProt: A0A2P6TMI2 |
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-Sugars , 2 types, 8 molecules
#35: Sugar | ChemComp-LMT / #36: Sugar | ChemComp-DGD / |
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+Non-polymers , 29 types, 494 molecules
-Details
Has ligand of interest | N |
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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 / Type: COMPLEX / Entity ID: #1-#23 / Source: NATURAL |
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Molecular weight | Value: 1 MDa / Experimental value: NO |
Source (natural) | Organism: Chlorella ohadii (plant) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Image recording | Average exposure time: 1.4 sec. / Electron dose: 49.05 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 4926 |
-Processing
Software |
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 553691 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185138 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 74.16 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6IJO | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.18 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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