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Yorodumi- PDB-8j7b: Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j7b | ||||||
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Title | Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI in state 2 (PSI-ST2) | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / photosystem / PLANT PROTEIN | ||||||
Function / homology | Function and homology information photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / plastoglobule / chloroplast membrane / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I ...photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / chloroplast stromal thylakoid / response to low light intensity stimulus / plastoglobule / chloroplast membrane / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å | ||||||
Authors | Chen, S.J.B. / Wu, J.H. / Sui, S.F. / Zhang, L.X. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2) Authors: Chen, S.J.B. / Wu, J.H. / Sui, S.F. / Zhang, L.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j7b.cif.gz | 889.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j7b.ent.gz | 768.2 KB | Display | PDB format |
PDBx/mmJSON format | 8j7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/8j7b ftp://data.pdbj.org/pub/pdb/validation_reports/j7/8j7b | HTTPS FTP |
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-Related structure data
Related structure data | 36037MC 8j6zC 8j7aC 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
-Chlorophyll a-b binding protein ... , 2 types, 2 molecules 14
#1: Protein | Mass: 26021.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHCA1, CAB6, At3g54890, F28P10.130 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q01667 |
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#4: Protein | Mass: 27760.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHCA4, CAB4, At3g47470, F1P2.20 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P27521 |
-Photosystem I chlorophyll a/b-binding protein ... , 2 types, 2 molecules 23
#2: Protein | Mass: 27782.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHCA2, At3g61470, F2A19.70 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SYW8 |
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#3: Protein | Mass: 29206.311 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LHCA3, At1g61520, T25B24.12 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SY97 |
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#5: Protein | Mass: 83315.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: psaA, AtCg00350 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P56766, photosystem I |
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#6: Protein | Mass: 82555.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: psaB, AtCg00340 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P56767, photosystem I |
-Photosystem I reaction center subunit ... , 9 types, 9 molecules DEFGHIJKL
#8: Protein | Mass: 22336.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAD2, At1g03130, F10O3_4 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SA56 |
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#9: Protein | Mass: 14984.955 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAE1, At4g28750, F16A16.140 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9S831 |
#10: Protein | Mass: 24203.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAF, At1g31330, T19E23.12 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SHE8 |
#11: Protein | Mass: 17103.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAG, At1g55670, F20N2.21, F20N2.33, F20N2_3 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9S7N7 |
#12: Protein | Mass: 15291.522 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAH2, At1g52230, F9I5.11 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI6 |
#13: Protein/peptide | Mass: 4137.024 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: psaI, AtCg00510 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P56768 |
#14: Protein/peptide | Mass: 5011.897 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: psaJ, AtCg00630 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P56769 |
#15: Protein | Mass: 13219.431 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAK, At1g30380, T4K22.2 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI5 |
#16: Protein | Mass: 23070.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSAL, At4g12800, T20K18.150 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI4 |
-Protein / Sugars , 2 types, 2 molecules C
#27: Sugar | ChemComp-DGD / |
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#7: Protein | Mass: 9049.509 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: psaC, frxA, AtCg01060 / Production host: Arabidopsis thaliana (thale cress) / References: UniProt: P62090, photosystem I |
-Non-polymers , 10 types, 200 molecules
#17: Chemical | ChemComp-CHL / #18: Chemical | ChemComp-CLA / #19: Chemical | #20: Chemical | ChemComp-LHG / #21: Chemical | ChemComp-LUT / ( #22: Chemical | ChemComp-BCR / #23: Chemical | #24: Chemical | ChemComp-CL0 / | #25: Chemical | #26: Chemical | |
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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: Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2) Type: COMPLEX / Source: NATURAL |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137602 / Symmetry type: POINT | ||||||||||||||||||||||||
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