+Open data
-Basic information
Entry | Database: PDB / ID: 6zoo | |||||||||||||||
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Title | Photosystem I reduced Plastocyanin Complex | |||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosystem I / membrane protein | |||||||||||||||
Function / homology | Function and homology information response to low light intensity stimulus / response to high light intensity / chloroplast thylakoid / plastoglobule / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope ...response to low light intensity stimulus / response to high light intensity / chloroplast thylakoid / plastoglobule / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / protein domain specific binding / copper ion binding / mRNA binding / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Pisum sativum (garden pea) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å | |||||||||||||||
Authors | Nelson, N. / Caspy, I. / Shkolnisky, Y. | |||||||||||||||
Funding support | Israel, Belgium, 4items
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Citation | Journal: Biochem J / Year: 2021 Title: Structure of plant photosystem I-plastocyanin complex reveals strong hydrophobic interactions. Authors: Ido Caspy / Mariia Fadeeva / Sebastian Kuhlgert / Anna Borovikova-Sheinker / Daniel Klaiman / Gal Masrati / Friedel Drepper / Nir Ben-Tal / Michael Hippler / Nathan Nelson / Abstract: Photosystem I is defined as plastocyanin-ferredoxin oxidoreductase. Taking advantage of genetic engineering, kinetic analyses and cryo-EM, our data provide novel mechanistic insights into binding and ...Photosystem I is defined as plastocyanin-ferredoxin oxidoreductase. Taking advantage of genetic engineering, kinetic analyses and cryo-EM, our data provide novel mechanistic insights into binding and electron transfer between PSI and Pc. Structural data at 2.74 Å resolution reveals strong hydrophobic interactions in the plant PSI-Pc ternary complex, leading to exclusion of water molecules from PsaA-PsaB/Pc interface once the PSI-Pc complex forms. Upon oxidation of Pc, a slight tilt of bound oxidized Pc allows water molecules to accommodate the space between Pc and PSI to drive Pc dissociation. Such a scenario is consistent with the six times larger dissociation constant of oxidized as compared with reduced Pc and mechanistically explains how this molecular machine optimized electron transfer for fast turnover. | |||||||||||||||
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 | 6zoo.cif.gz | 850.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zoo.ent.gz | 779.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zoo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zoo_validation.pdf.gz | 10.6 MB | Display | wwPDB validaton report |
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Full document | 6zoo_full_validation.pdf.gz | 11.4 MB | Display | |
Data in XML | 6zoo_validation.xml.gz | 229.2 KB | Display | |
Data in CIF | 6zoo_validation.cif.gz | 277 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/6zoo ftp://data.pdbj.org/pub/pdb/validation_reports/zo/6zoo | HTTPS FTP |
-Related structure data
Related structure data | 11326MC 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, 2 molecules AB
#1: Protein | Mass: 82717.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0F6NFW5, photosystem I |
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#2: Protein | Mass: 82381.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0F6NGI2, photosystem I |
-Protein , 7 types, 7 molecules CDEGL2P
#3: Protein | Mass: 8860.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P10793, photosystem I |
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#4: Protein | Mass: 16041.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K8 |
#5: Protein | Mass: 7479.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K6 |
#7: Protein | Mass: 10678.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0M3KL13 |
#12: Protein | Mass: 16863.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) |
#14: Protein | Mass: 22845.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q41038 |
#17: Protein | Mass: 10353.487 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P16002 |
-Photosystem I reaction center subunit ... , 5 types, 5 molecules FHIJK
#6: Protein | Mass: 17137.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0M3KL12 |
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#8: Protein | Mass: 10043.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) |
#9: Protein/peptide | Mass: 3409.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P17227 |
#10: Protein/peptide | Mass: 4767.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAL3 |
#11: Protein | Mass: 8135.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L3 |
-Chlorophyll a-b binding protein ... , 3 types, 3 molecules 134
#13: Protein | Mass: 21335.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q01667 |
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#15: Protein | Mass: 24139.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q32904 |
#16: Protein | Mass: 21994.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9SQL2 |
-Sugars , 2 types, 13 molecules
#24: Sugar | ChemComp-LMT / #27: Sugar | ChemComp-DGD / |
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-Non-polymers , 14 types, 232 molecules
#18: Chemical | ChemComp-CL0 / | ||||||||||||||||||||||||
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#19: Chemical | ChemComp-CLA / #20: Chemical | #21: Chemical | #22: Chemical | ChemComp-BCR / #23: Chemical | ChemComp-LHG / #25: Chemical | ChemComp-LMG / #26: Chemical | #28: Chemical | ChemComp-LUT / ( #29: Chemical | ChemComp-CHL / #30: Chemical | #31: Chemical | ChemComp-3PH / | #32: Chemical | ChemComp-CU / | #33: Water | ChemComp-HOH / | |
-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 plastocyanin complex / Type: COMPLEX / Entity ID: #1, #10-#11, #13-#14, #16-#17, #2-#7, #9 / Source: NATURAL |
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Molecular weight | Value: 0.65 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Pisum sativum (garden pea) |
Buffer solution | pH: 7 / Details: 20mM Mes-Tris, 10mM sodium ascorbate |
Specimen | Conc.: 2.8 mg/ml / 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: 130000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 300 nm / Calibrated defocus min: 300 nm / Calibrated defocus max: 1500 nm / C2 aperture diameter: 20 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2.49 sec. / Electron dose: 40.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 6129 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 359977 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104127 / Num. of class averages: 4 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 38.8 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6YEZ | ||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.84 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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