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Yorodumi- PDB-3jcu: Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angst... -
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Entry | Database: PDB / ID: 3jcu | ||||||
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Title | Cryo-EM structure of spinach PSII-LHCII supercomplex at 3.2 Angstrom resolution | ||||||
Components |
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Keywords | MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information chloroplast photosystem II / photosynthesis, light harvesting / plastoglobule / : / photosystem II oxygen evolving complex / photosystem II assembly / photosynthesis, light harvesting in photosystem I / oxygen evolving activity / photosystem II stabilization / photosystem II ...chloroplast photosystem II / photosynthesis, light harvesting / plastoglobule / : / photosystem II oxygen evolving complex / photosystem II assembly / photosynthesis, light harvesting in photosystem I / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / : / chloroplast envelope / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / photosynthetic electron transport chain / response to herbicide / photosystem II / extrinsic component of membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / chloroplast thylakoid membrane / response to light stimulus / photosynthetic electron transport in photosystem II / photosynthesis / phosphoprotein binding / membrane => GO:0016020 / protein stabilization / electron transfer activity / iron ion binding / calcium ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Spinacia oleracea (spinach) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Wei, X.P. / Zhang, X.Z. / Su, X.D. / Cao, P. / Liu, X.Y. / Li, M. / Chang, W.R. / Liu, Z.F. | ||||||
Citation | Journal: Nature / Year: 2016 Title: Structure of spinach photosystem II-LHCII supercomplex at 3.2 Å resolution. Authors: Xuepeng Wei / Xiaodong Su / Peng Cao / Xiuying Liu / Wenrui Chang / Mei Li / Xinzheng Zhang / Zhenfeng Liu / Abstract: During photosynthesis, the plant photosystem II core complex receives excitation energy from the peripheral light-harvesting complex II (LHCII). The pathways along which excitation energy is ...During photosynthesis, the plant photosystem II core complex receives excitation energy from the peripheral light-harvesting complex II (LHCII). The pathways along which excitation energy is transferred between them, and their assembly mechanisms, remain to be deciphered through high-resolution structural studies. Here we report the structure of a 1.1-megadalton spinach photosystem II-LHCII supercomplex solved at 3.2 Å resolution through single-particle cryo-electron microscopy. The structure reveals a homodimeric supramolecular system in which each monomer contains 25 protein subunits, 105 chlorophylls, 28 carotenoids and other cofactors. Three extrinsic subunits (PsbO, PsbP and PsbQ), which are essential for optimal oxygen-evolving activity of photosystem II, form a triangular crown that shields the Mn4CaO5-binding domains of CP43 and D1. One major trimeric and two minor monomeric LHCIIs associate with each core-complex monomer, and the antenna-core interactions are reinforced by three small intrinsic subunits (PsbW, PsbH and PsbZ). By analysing the closely connected interfacial chlorophylls, we have obtained detailed insights into the energy-transfer pathways between the antenna and core complexes. | ||||||
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 3jcu.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3jcu.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 3jcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jcu_validation.pdf.gz | 13.8 MB | Display | wwPDB validaton report |
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Full document | 3jcu_full_validation.pdf.gz | 14.7 MB | Display | |
Data in XML | 3jcu_validation.xml.gz | 330.5 KB | Display | |
Data in CIF | 3jcu_validation.cif.gz | 419.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/3jcu ftp://data.pdbj.org/pub/pdb/validation_reports/jc/3jcu | HTTPS FTP |
-Related structure data
Related structure data | 6617MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
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Deposited unit |
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-Components
-Photosystem II ... , 13 types, 26 molecules AaBbCcDdHhJjKkMmTtUuWwXxZz
#1: Protein | Mass: 38134.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P69560 #2: Protein | Mass: 56207.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P04160 #3: Protein | Mass: 51880.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06003 #4: Protein | Mass: 39535.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06005 #8: Protein | Mass: 7735.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P05146 #10: Protein/peptide | Mass: 4117.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3L2 #11: Protein | Mass: 6751.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12163 #13: Protein/peptide | Mass: 3783.538 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P62112 #19: Protein/peptide | Mass: 3825.642 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P61840 #20: Protein | Mass: 10676.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RHP1 #21: Protein | Mass: 14186.097 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q41387 #22: Protein | Mass: 11958.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RTU3, UniProt: A0A0K9RHP1*PLUS #23: Protein | Mass: 6541.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3M6 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9393.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P69383 #6: Protein/peptide | Mass: 4502.351 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P60128 |
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-Protein Photosystem II reaction center protein ... , 2 types, 4 molecules IiLl
#9: Protein/peptide | Mass: 4170.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P62103 #12: Protein/peptide | Mass: 4498.100 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P60150 |
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-Oxygen-evolving enhancer protein ... , 3 types, 6 molecules OoPpQq
#14: Protein | Mass: 35207.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12359 #15: Protein | Mass: 28495.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12302 #16: Protein | Mass: 24884.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12301 |
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-Chlorophyll A-B Binding protein ... , 2 types, 4 molecules RrSs
#17: Protein | Mass: 26735.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: F2Z293, UniProt: A0A0K9QLX6*PLUS #18: Protein | Mass: 31341.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9QUQ7 |
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-Protein / Sugars , 2 types, 14 molecules GNYgny
#32: Sugar | ChemComp-DGD / #7: Protein | Mass: 28449.391 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12333 |
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-Non-polymers , 16 types, 314 molecules
#24: Chemical | #25: Chemical | #26: Chemical | ChemComp-CL / #27: Chemical | ChemComp-CLA / #28: Chemical | ChemComp-PHO / #29: Chemical | ChemComp-BCR / #30: Chemical | ChemComp-SQD / #31: Chemical | ChemComp-LMG / #33: Chemical | #34: Chemical | #35: Chemical | ChemComp-LHG / #36: Chemical | #37: Chemical | ChemComp-CHL / #38: Chemical | ChemComp-LUT / ( #39: Chemical | ChemComp-XAT / ( #40: Chemical | ChemComp-NEX / ( |
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