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Yorodumi- PDB-4xk8: Crystal structure of plant photosystem I-LHCI super-complex at 2.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xk8 | ||||||
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Title | Crystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / photosystem i / plant LHCI-PSI supercomplex | ||||||
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 / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / oxidoreductase activity / electron transfer activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pisum sativum (garden pea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Suga, M. / Qin, X. / Kuang, T. / Shen, J.R. | ||||||
Citation | Journal: Science / Year: 2015 Title: Photosynthesis. Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex. Authors: Xiaochun Qin / Michihiro Suga / Tingyun Kuang / Jian-Ren Shen / Abstract: Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by ...Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by a large light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core with extremely high efficiency. We report the structure of PSI-LHCI, a 600-kilodalton membrane protein supercomplex, from Pisum sativum (pea) at a resolution of 2.8 angstroms. The structure reveals the detailed arrangement of pigments and other cofactors—especially within LHCI—as well as numerous specific interactions between the PSI core and LHCI. These results provide a firm structural basis for our understanding on the energy transfer and photoprotection mechanisms within the PSI-LHCI supercomplex. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xk8.cif.gz | 3.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4xk8.ent.gz | 3 MB | Display | PDB format |
PDBx/mmJSON format | 4xk8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xk8_validation.pdf.gz | 91.7 MB | Display | wwPDB validaton report |
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Full document | 4xk8_full_validation.pdf.gz | 94.3 MB | Display | |
Data in XML | 4xk8_validation.xml.gz | 419.7 KB | Display | |
Data in CIF | 4xk8_validation.cif.gz | 492.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/4xk8 ftp://data.pdbj.org/pub/pdb/validation_reports/xk/4xk8 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 4 molecules AaBb
#1: Protein | Mass: 82408.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: P05310*PLUS #2: Protein | Mass: 82466.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: P05311*PLUS |
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-Protein , 3 types, 6 molecules CcDd27
#3: Protein | Mass: 8860.276 Da / Num. of mol.: 2 / Fragment: UNP residues 2-81 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: P10793, photosystem I #4: Protein | Mass: 15853.142 Da / Num. of mol.: 2 / Fragment: UNP residues 63-203 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: I1NGD2, UniProt: A5Z2K3*PLUS #14: Protein | Mass: 22693.666 Da / Num. of mol.: 2 / Fragment: UNP residues 62-267 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: Q41038 |
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-Putative uncharacterized ... , 3 types, 6 molecules EeHhLl
#5: Protein | Mass: 7299.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: E1C9K6*PLUS #8: Protein | Mass: 9639.886 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: C6T221*PLUS #12: Protein | Mass: 16130.484 Da / Num. of mol.: 2 / Fragment: UNP residues 4-156 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: E1C9L1 |
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-Photosystem I reaction center subunit ... , 5 types, 10 molecules FfGgIiJjKk
#6: Protein | Mass: 17009.771 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: P12355*PLUS #7: Protein | Mass: 10460.736 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: P12357*PLUS #9: Protein/peptide | Mass: 3296.041 Da / Num. of mol.: 2 / Fragment: UNP residues 2-31 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: P17227 #10: Protein/peptide | Mass: 4402.227 Da / Num. of mol.: 2 / Fragment: UNP residues 1-39 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: A4GGC6 #11: Protein | Mass: 8462.847 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: E1C9L3 |
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-Chlorophyll a-b binding protein ... , 3 types, 6 molecules 163849
#13: Protein | Mass: 21354.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: Q01667*PLUS #15: Protein | Mass: 23725.020 Da / Num. of mol.: 2 / Fragment: UNP residues 55-272 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: Q32904 #16: Protein | Mass: 21719.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: Q9SQL2*PLUS |
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-Sugars , 3 types, 9 molecules
#22: Sugar | ChemComp-HTG / #23: Sugar | ChemComp-LMT / | #24: Sugar | |
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-Non-polymers , 10 types, 590 molecules
#17: Chemical | ChemComp-CLA / #18: Chemical | ChemComp-PQN / #19: Chemical | ChemComp-LHG / #20: Chemical | ChemComp-BCR / #21: Chemical | ChemComp-SF4 / #25: Chemical | ChemComp-LMG / #26: Chemical | ChemComp-CHL / #27: Chemical | ChemComp-LUT / ( #28: Chemical | ChemComp-XAT / ( #29: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.59 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion / Details: PEG |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 268282 / % possible obs: 99.8 % / Redundancy: 7.5 % / Net I/σ(I): 7 |
-Processing
Software |
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Refinement | Resolution: 2.8→49.147 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→49.147 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -28.0049 Å / Origin y: -0.025 Å / Origin z: 145.821 Å
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Refinement TLS group | Selection details: all |