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Yorodumi- EMDB-6617: CryoEM map of spinach PSII-LHCII supercomplex at 3.2A resolution -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6617 | |||||||||
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Title | CryoEM map of spinach PSII-LHCII supercomplex at 3.2A resolution | |||||||||
Map data | A cryo-EM map of a membrane protein complex | |||||||||
Sample |
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Keywords | membrane protein / spinach photosystem II / cryo-EM | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Wei XP / Zhang XZ / Su XD / Cao P / Liu XY / Li M / Chang WR / Liu ZF | |||||||||
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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6617.map.gz | 7.9 MB | EMDB map data format | |
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Header (meta data) | emd-6617-v30.xml emd-6617.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | 400_6617.gif 80_6617.gif | 60.6 KB 13.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6617 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6617 | HTTPS FTP |
-Validation report
Summary document | emd_6617_validation.pdf.gz | 307.5 KB | Display | EMDB validaton report |
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Full document | emd_6617_full_validation.pdf.gz | 307.1 KB | Display | |
Data in XML | emd_6617_validation.xml.gz | 4.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6617 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6617 | HTTPS FTP |
-Related structure data
Related structure data | 3jcuMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6617.map.gz / Format: CCP4 / Size: 37.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | A cryo-EM map of a membrane protein complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Spinach PSII-LHCII supercomplex
Entire | Name: Spinach PSII-LHCII supercomplex |
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Components |
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-Supramolecule #1000: Spinach PSII-LHCII supercomplex
Supramolecule | Name: Spinach PSII-LHCII supercomplex / type: sample / ID: 1000 / Oligomeric state: homodimer / Number unique components: 1 |
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Molecular weight | Experimental: 1.1 MDa / Theoretical: 1.1 MDa |
-Macromolecule #1: Photosystem II (or water-plastoquinone oxidoreductase) in complex...
Macromolecule | Name: Photosystem II (or water-plastoquinone oxidoreductase) in complex with Light harvesting complex II type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Spinacia oleracea (spinach) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Grid | Details: 400 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Nov 20, 2015 |
Image recording | Category: CCD / Film or detector model: OTHER / Number real images: 1774 / Average electron dose: 50 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: OTHER / Software - Name: EMAN, RELION / Number images used: 109042 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera, Coot |
Refinement | Space: REAL |
Output model | PDB-3jcu: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: Phenix |
Refinement | Space: REAL |
Output model | PDB-3jcu: |
-Atomic model buiding 3
Initial model | PDB ID: |
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Software | Name: Phenix |
Refinement | Space: REAL |
Output model | PDB-3jcu: |