+Open data
-Basic information
Entry | Database: PDB / ID: 8bcv | ||||||||||||
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Title | Photosystem I assembly intermediate of Avena sativa | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / PSI structure / assembly intermediate / Monocotyledons / etiolation | ||||||||||||
Function / homology | Function and homology information photosynthesis, light harvesting / thylakoid membrane / chloroplast thylakoid / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis ...photosynthesis, light harvesting / thylakoid membrane / chloroplast thylakoid / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Avena sativa (oats) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | ||||||||||||
Authors | Naschberger, A. / Amunts, A. / Nelson, N. | ||||||||||||
Funding support | Sweden, Israel, 3items
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Citation | Journal: To Be Published Title: Photosystem I assembly intermediate of Avena sativa Authors: Naschberger, A. / Amunts, A. / Nelson, N. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bcv.cif.gz | 849.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bcv.ent.gz | 739.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bcv_validation.pdf.gz | 10.5 MB | Display | wwPDB validaton report |
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Full document | 8bcv_full_validation.pdf.gz | 11 MB | Display | |
Data in XML | 8bcv_validation.xml.gz | 135.9 KB | Display | |
Data in CIF | 8bcv_validation.cif.gz | 191.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/8bcv ftp://data.pdbj.org/pub/pdb/validation_reports/bc/8bcv | HTTPS FTP |
-Related structure data
Related structure data | 15969MC 8bcwC 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: 83263.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) / References: UniProt: A0A3G1AUL2, photosystem I |
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#2: Protein | Mass: 82605.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) / References: UniProt: A0A3G1AZK6, photosystem I |
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 8909.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) / References: UniProt: A0A3G1ATU7, photosystem I |
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-Photosystem I reaction center subunit ... , 9 types, 9 molecules DEHILFGJK
#4: Protein | Mass: 22081.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) |
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#5: Protein | Mass: 15298.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) |
#6: Protein | Mass: 10088.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) |
#7: Protein/peptide | Mass: 3995.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) / References: UniProt: A0A3G1AZM6 |
#8: Protein | Mass: 22575.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) |
#9: Protein | Mass: 19346.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) |
#10: Protein | Mass: 15113.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) |
#11: Protein | Mass: 5849.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) |
#12: Protein | Mass: 13583.741 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) |
-Chlorophyll a-b binding protein ... , 4 types, 4 molecules 1234
#13: Protein | Mass: 26137.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) / References: UniProt: A0A482JYH1 |
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#14: Protein | Mass: 22706.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) |
#15: Protein | Mass: 29344.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) |
#16: Protein | Mass: 27786.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Avena sativa (oats) |
-Sugars , 2 types, 21 molecules
#24: Sugar | ChemComp-LMU / #25: Sugar | |
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-Non-polymers , 13 types, 906 molecules
#17: Chemical | #18: Chemical | ChemComp-CLA / #19: Chemical | #20: Chemical | ChemComp-LHG / #21: Chemical | ChemComp-BCR / #22: Chemical | #23: Chemical | ChemComp-LMG / #26: Chemical | ChemComp-LUT / ( #27: Chemical | ChemComp-CHL / #28: Chemical | #29: Chemical | ChemComp-C7Z / ( | #30: Chemical | ChemComp-QDL / | #31: 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: Assembly Intermediate of PSI from Avena sativa / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Avena sativa (oats) |
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: 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 defocus max: 2100 nm / Nominal defocus min: 300 nm |
Image recording | Electron dose: 51.346 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96997 / Symmetry type: POINT | ||||||||||||||||||||||||
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