+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31062 | |||||||||||||||||||||
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Title | Structure of monomeric photosystem II | |||||||||||||||||||||
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: 2.78 Å | |||||||||||||||||||||
Authors | Yu H / Hamaguchi T / Nakajima Y / Kato K / kawakami K / Akita F / Yonekura K / Shen JR | |||||||||||||||||||||
Funding support | Japan, 6 items
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Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2021 Title: Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer. Authors: Huaxin Yu / Tasuku Hamaguchi / Yoshiki Nakajima / Koji Kato / Keisuke Kawakami / Fusamichi Akita / Koji Yonekura / Jian-Ren Shen / Abstract: Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The ...Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The crystal structure of monomeric PSII has been solved at 3.6 Å resolution, but it is still not clear which factors contribute to the formation of the dimer. Here, we solved the structure of PSII monomer at a resolution of 2.78 Å using cryo-electron microscopy (cryo-EM). From our cryo-EM density map, we observed apparent differences in pigments and lipids in the monomer-monomer interface between the PSII monomer and dimer. One β-carotene and two sulfoquinovosyl diacylglycerol (SQDG) molecules are found in the monomer-monomer interface of the dimer structure but not in the present monomer structure, although some SQDG and other lipid molecules are found in the analogous region of the low-resolution crystal structure of the monomer, or cryo-EM structure of an apo-PSII monomer lacking the extrinsic proteins from Synechocystis sp. PCC 6803. In the current monomer structure, a large part of the PsbO subunit was also found to be disordered. These results indicate the importance of the β-carotene, SQDG and PsbO in formation of the PSII dimer. | |||||||||||||||||||||
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_31062.map.gz | 7.5 MB | EMDB map data format | |
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Header (meta data) | emd-31062-v30.xml emd-31062.xml | 37.2 KB 37.2 KB | Display Display | EMDB header |
Images | emd_31062.png | 217 KB | ||
Masks | emd_31062_msk_1.map | 52.7 MB | Mask map | |
Others | emd_31062_half_map_1.map.gz emd_31062_half_map_2.map.gz | 40.7 MB 40.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31062 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31062 | HTTPS FTP |
-Validation report
Summary document | emd_31062_validation.pdf.gz | 783.9 KB | Display | EMDB validaton report |
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Full document | emd_31062_full_validation.pdf.gz | 783.5 KB | Display | |
Data in XML | emd_31062_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | emd_31062_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31062 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31062 | HTTPS FTP |
-Related structure data
Related structure data | 7edaMC 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_31062.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82192 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_31062_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_31062_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31062_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Photosystem II
+Supramolecule #1: Photosystem II
+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: CHLOROPHYLL A
+Macromolecule #24: PHEOPHYTIN A
+Macromolecule #25: BETA-CAROTENE
+Macromolecule #26: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #27: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+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: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #31: BICARBONATE ION
+Macromolecule #32: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #33: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #34: (3R)-beta,beta-caroten-3-ol
+Macromolecule #35: HEME C
+Macromolecule #36: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 173875 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |