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Yorodumi- EMDB-13078: Structure of C2S2M2-type Photosystem supercomplex from Arabidopsi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13078 | |||||||||
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Title | Structure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana (digitonin-extracted) | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information plastid thylakoid membrane / : / photoinhibition / photosystem II antenna complex / photosynthesis, light harvesting in photosystem II / nonphotochemical quenching / sequestering of metal ion / PSII associated light-harvesting complex II / chloroplast stromal thylakoid / thylakoid lumen ...plastid thylakoid membrane / : / photoinhibition / photosystem II antenna complex / photosynthesis, light harvesting in photosystem II / nonphotochemical quenching / sequestering of metal ion / PSII associated light-harvesting complex II / chloroplast stromal thylakoid / thylakoid lumen / response to high light intensity / thylakoid membrane / regulation of stomatal movement / chloroplast thylakoid / plastoglobule / vacuolar transport / chloroplast thylakoid lumen / photosystem II oxygen evolving complex / photosystem II assembly / response to abscisic acid / photosynthesis, light harvesting in photosystem I / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / : / thylakoid / apoplast / chloroplast envelope / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem I / photosynthetic electron transport chain / poly(U) RNA binding / response to herbicide / photosystem II / plastid / chloroplast stroma / 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 / chloroplast / membrane => GO:0016020 / endosome / protein stabilization / electron transfer activity / iron ion binding / protein domain specific binding / mRNA binding / heme binding / endoplasmic reticulum / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) / Mouse-ear cress (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.79 Å | |||||||||
Authors | Graca AT / Hall M / Persson K / Schroder WP | |||||||||
Funding support | Sweden, 2 items
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Citation | Journal: Sci Rep / Year: 2021 Title: High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction. Authors: André T Graça / Michael Hall / Karina Persson / Wolfgang P Schröder / Abstract: In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the ...In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated MnCaO-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Afonine PV / Poon BK / Read RJ / Sobolev OV / Terwilliger TC / Urzhumtsev A / Adams PD | |||||||||
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_13078.map.gz | 383.2 MB | EMDB map data format | |
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Header (meta data) | emd-13078-v30.xml emd-13078.xml | 46.6 KB 46.6 KB | Display Display | EMDB header |
Images | emd_13078.png | 223.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13078 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13078 | HTTPS FTP |
-Validation report
Summary document | emd_13078_validation.pdf.gz | 266.8 KB | Display | EMDB validaton report |
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Full document | emd_13078_full_validation.pdf.gz | 265.9 KB | Display | |
Data in XML | emd_13078_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | emd_13078_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13078 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13078 | HTTPS FTP |
-Related structure data
Related structure data | 7ouiMC 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_13078.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82 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 : Photosystem II - Light Harvesting Complex II supercomplex (PSII-L...
+Supramolecule #1: Photosystem II - Light Harvesting Complex II supercomplex (PSII-L...
+Supramolecule #2: CP24-LHCII (M-trimer)
+Supramolecule #3: LHCII S-trimer
+Supramolecule #4: CP29
+Supramolecule #5: CP26
+Supramolecule #6: Photosystem II core complex (dimer)
+Macromolecule #1: Lhcb1.4
+Macromolecule #2: Lhcb3.1
+Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #4: Photosystem II protein D1
+Macromolecule #5: Photosystem II CP47 reaction center protein
+Macromolecule #6: Photosystem II CP43 reaction center protein
+Macromolecule #7: Photosystem II D2 protein
+Macromolecule #8: Cytochrome b559 subunit alpha
+Macromolecule #9: Cytochrome b559 subunit beta (PsbF)
+Macromolecule #10: Photosystem II reaction center protein H
+Macromolecule #11: Photosystem II reaction center protein I
+Macromolecule #12: Photosystem II reaction center protein K
+Macromolecule #13: Photosystem II reaction center protein L
+Macromolecule #14: Photosystem II reaction center protein M
+Macromolecule #15: Oxygen-evolving enhancer protein 1-1, chloroplastic
+Macromolecule #16: Photosystem II reaction center protein T
+Macromolecule #17: Photosystem II reaction center W protein, chloroplastic
+Macromolecule #18: PsbX
+Macromolecule #19: Photosystem II reaction center protein Z
+Macromolecule #20: Chlorophyll a-b binding protein CP26, chloroplastic
+Macromolecule #21: Chlorophyll a-b binding protein 1, chloroplastic
+Macromolecule #22: Chlorophyll a-b binding protein CP29.1, chloroplastic
+Macromolecule #23: PsbTn
+Macromolecule #24: CHLOROPHYLL B
+Macromolecule #25: CHLOROPHYLL A
+Macromolecule #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #27: PHEOPHYTIN A
+Macromolecule #28: BETA-CAROTENE
+Macromolecule #29: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #30: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #31: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #32: Digitonin
+Macromolecule #33: BICARBONATE ION
+Macromolecule #34: FE (II) ION
+Macromolecule #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #36: CALCIUM ION
+Macromolecule #37: CHLORIDE ION
+Macromolecule #38: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #39: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #40: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...
+Macromolecule #41: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #42: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 / Component - Name: HEPES-KOH / Details: 10mM HEPES-KOH pH7.5 + 0.01% (w/v) digitonin |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Details: 50 mA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force -5 Wait time 1s Blotting time 5s. |
Details | Indicated sample concentration based on Chlorophyll measurement. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 12227 / Average electron dose: 1.49 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |