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Yorodumi- EMDB-24239: High-resolution structure of photosystem II from the mesophilic c... -
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-Basic information
Entry | Database: EMDB / ID: EMD-24239 | |||||||||
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Title | High-resolution structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803 | |||||||||
Map data | Photosystem II from Synechocystis 6803 full dose unsharpened | |||||||||
Sample |
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Function / homology | Function and homology information plasma membrane-derived thylakoid 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 ...plasma membrane-derived thylakoid 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 / calcium ion binding / heme binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) / Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.93 Å | |||||||||
Authors | Gisriel CJ / Brudvig GW | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, sp. PCC 6803. Authors: Christopher J Gisriel / Jimin Wang / Jinchan Liu / David A Flesher / Krystle M Reiss / Hao-Li Huang / Ke R Yang / William H Armstrong / M R Gunner / Victor S Batista / Richard J Debus / Gary W Brudvig / Abstract: Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium sp. PCC 6803 has provided insights into the mechanism of ...Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a high-resolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the D1 subunit is flexible, some waters near the active site are partially occupied, and differences in the PsbV subunit block the Large (O1) water channel. These features strongly influence the structural picture of PSII, especially as it pertains to the mechanism of water oxidation. | |||||||||
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_24239.map.gz | 29.2 MB | EMDB map data format | |
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Header (meta data) | emd-24239-v30.xml emd-24239.xml | 37.6 KB 37.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24239_fsc.xml | 13.5 KB | Display | FSC data file |
Images | emd_24239.png | 52.8 KB | ||
Others | emd_24239_additional_1.map.gz | 169.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24239 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24239 | HTTPS FTP |
-Validation report
Summary document | emd_24239_validation.pdf.gz | 393.4 KB | Display | EMDB validaton report |
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Full document | emd_24239_full_validation.pdf.gz | 392.9 KB | Display | |
Data in XML | emd_24239_validation.xml.gz | 13 KB | Display | |
Data in CIF | emd_24239_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24239 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24239 | HTTPS FTP |
-Related structure data
Related structure data | 7n8oMC 7rcvC 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_24239.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Photosystem II from Synechocystis 6803 full dose unsharpened | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Photosystem II from Synechocystis 6803 full dose sharpened
File | emd_24239_additional_1.map | ||||||||||||
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Annotation | Photosystem II from Synechocystis 6803 full dose sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Photosystem II
+Supramolecule #1: Photosystem II
+Macromolecule #1: Photosystem II protein D1 2
+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: Sll1638 protein
+Macromolecule #15: Photosystem II protein Y
+Macromolecule #16: Photosystem II reaction center protein T
+Macromolecule #17: Photosystem II 12 kDa extrinsic protein
+Macromolecule #18: Cytochrome c-550
+Macromolecule #19: Photosystem II reaction center X protein
+Macromolecule #20: Photosystem II reaction center protein Ycf12
+Macromolecule #21: Photosystem II reaction center protein Z
+Macromolecule #22: CA-MN4-O5 CLUSTER
+Macromolecule #23: FE (II) ION
+Macromolecule #24: CHLORIDE ION
+Macromolecule #25: CHLOROPHYLL A
+Macromolecule #26: PHEOPHYTIN A
+Macromolecule #27: BETA-CAROTENE
+Macromolecule #28: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #29: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #30: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #31: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #32: BICARBONATE ION
+Macromolecule #33: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #34: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #35: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #36: CALCIUM ION
+Macromolecule #37: (3R)-beta,beta-caroten-3-ol
+Macromolecule #38: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |