+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30547 | |||||||||
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Title | Cryo-EM Structure of PSII at 1.95 angstrom resolution | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / extrinsic component of membrane / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthetic electron transport in photosystem II / photosynthesis / respiratory electron transport chain / manganese ion binding / protein stabilization / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermosynechococcus vulcanus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.95 Å | |||||||||
Authors | Kato K / Miyazaki N / Hamaguchi T / Nakajima Y / Akita F / Yonekura K / Shen JR | |||||||||
Citation | Journal: Commun Biol / Year: 2021 Title: High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams. Authors: Koji Kato / Naoyuki Miyazaki / Tasuku Hamaguchi / Yoshiki Nakajima / Fusamichi Akita / Koji Yonekura / Jian-Ren Shen / Abstract: Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are ...Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins. | |||||||||
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_30547.map.gz | 21.4 MB | EMDB map data format | |
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Header (meta data) | emd-30547-v30.xml emd-30547.xml | 39.1 KB 39.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30547_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_30547.png | 66.9 KB | ||
Others | emd_30547_half_map_1.map.gz emd_30547_half_map_2.map.gz | 192 MB 192 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30547 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30547 | HTTPS FTP |
-Validation report
Summary document | emd_30547_validation.pdf.gz | 717 KB | Display | EMDB validaton report |
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Full document | emd_30547_full_validation.pdf.gz | 716.6 KB | Display | |
Data in XML | emd_30547_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | emd_30547_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30547 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30547 | HTTPS FTP |
-Related structure data
Related structure data | 7d1tMC 7d1uC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10556 (Title: Cryo-EM Structure of PSII at 1.95 angstrom resolution Data size: 427.6 Data #1: Unaligned multi-frame micrographs of PSII recorded by CRYO ARM 300 [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30547.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_30547_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_30547_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : PSII dimer
+Supramolecule #1: PSII dimer
+Macromolecule #1: Photosystem II protein D1
+Macromolecule #2: Photosystem II CP47 reaction center protein
+Macromolecule #3: Photosystem II CP43 reaction center protein
+Macromolecule #4: Photosystem II D2 protein
+Macromolecule #5: Cytochrome b559 subunit alpha
+Macromolecule #6: Cytochrome b559 subunit beta
+Macromolecule #7: Photosystem II reaction center protein H
+Macromolecule #8: Photosystem II reaction center protein I
+Macromolecule #9: Photosystem II reaction center protein J
+Macromolecule #10: Photosystem II reaction center protein K
+Macromolecule #11: Photosystem II reaction center protein L
+Macromolecule #12: Photosystem II reaction center protein M
+Macromolecule #13: Photosystem II manganese-stabilizing polypeptide
+Macromolecule #14: Photosystem II reaction center protein T
+Macromolecule #15: Photosystem II 12 kDa extrinsic protein
+Macromolecule #16: Cytochrome c-550
+Macromolecule #17: Photosystem II reaction center protein Ycf12
+Macromolecule #18: Photosystem II reaction center protein X
+Macromolecule #19: Photosystem II reaction center protein Z
+Macromolecule #20: Photosystem II protein Y
+Macromolecule #21: CA-MN4-O5 CLUSTER
+Macromolecule #22: FE (II) ION
+Macromolecule #23: CHLORIDE ION
+Macromolecule #24: CHLOROPHYLL A
+Macromolecule #25: PHEOPHYTIN A
+Macromolecule #26: BETA-CAROTENE
+Macromolecule #27: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #28: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #29: UNKNOWN LIGAND
+Macromolecule #30: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #31: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #32: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #33: BICARBONATE ION
+Macromolecule #34: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #35: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: HEME C
+Macromolecule #38: (3R)-beta,beta-caroten-3-ol
+Macromolecule #39: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.0 mg/mL | ||||||
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Buffer | pH: 6 / Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 83.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |