[English] 日本語
Yorodumi- EMDB-50019: cryoEM structure of Photosystem II averaged across S2-S3 states a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50019 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | cryoEM structure of Photosystem II averaged across S2-S3 states at 1.71 Angstrom resolution | ||||||||||||
Map data | The original map before sharpening | ||||||||||||
Sample |
| ||||||||||||
Keywords | Photosystem II core complex / Mn cluster / water oxidation / METAL BINDING PROTEIN | ||||||||||||
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 / extrinsic component of membrane ...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 / extrinsic component of membrane / photosystem II / photosynthesis, light reaction / phosphate ion binding / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Thermosynechococcus vestitus BP-1 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.71 Å | ||||||||||||
Authors | Hussein R / Graca A / Zouni A / Messinger J / Schroder WP | ||||||||||||
Funding support | Sweden, Germany, 3 items
| ||||||||||||
Citation | Journal: Science / Year: 2024 Title: Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II. Authors: Rana Hussein / André Graça / Jack Forsman / A Orkun Aydin / Michael Hall / Julia Gaetcke / Petko Chernev / Petra Wendler / Holger Dobbek / Johannes Messinger / Athina Zouni / Wolfgang P Schröder / Abstract: Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation ...Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation to molecular oxygen and plastoquinone reduction. Coupling of electron and proton transfer is crucial for efficiency; however, the molecular basis of these processes remains speculative owing to uncertain water binding sites and the lack of experimentally determined hydrogen positions. We thus collected high-resolution cryo-electron microscopy data of fully hydrated photosystem II from the thermophilic cyanobacterium to a final resolution of 1.71 angstroms. The structure reveals several previously undetected partially occupied water binding sites and more than half of the hydrogen and proton positions. This clarifies the pathways of substrate water binding and plastoquinone B protonation. | ||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_50019.map.gz | 716.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-50019-v30.xml emd-50019.xml | 43 KB 43 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_50019_fsc.xml | 23.7 KB | Display | FSC data file |
Images | emd_50019.png | 160.1 KB | ||
Filedesc metadata | emd-50019.cif.gz | 9.5 KB | ||
Others | emd_50019_additional_1.map.gz emd_50019_half_map_1.map.gz emd_50019_half_map_2.map.gz | 1.3 GB 1.3 GB 1.3 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50019 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50019 | HTTPS FTP |
-Validation report
Summary document | emd_50019_validation.pdf.gz | 984.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_50019_full_validation.pdf.gz | 984.3 KB | Display | |
Data in XML | emd_50019_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | emd_50019_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50019 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50019 | HTTPS FTP |
-Related structure data
Related structure data | 9evxMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_50019.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | The original map before sharpening | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.574 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: The sharpened map. The one used for analysis.
File | emd_50019_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | The sharpened map. The one used for analysis. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_50019_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_50019_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : dimeric core complex of PSII dPSII
+Supramolecule #1: dimeric core complex of PSII dPSII
+Macromolecule #1: Photosystem II protein D1 1
+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 X protein
+Macromolecule #18: Photosystem II reaction center protein Ycf12
+Macromolecule #19: Photosystem II reaction center protein Z
+Macromolecule #20: FE (II) ION
+Macromolecule #21: CHLORIDE ION
+Macromolecule #22: CHLOROPHYLL A
+Macromolecule #23: BETA-CAROTENE
+Macromolecule #24: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #25: STEARIC ACID
+Macromolecule #26: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #27: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #28: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #29: CA-MN4-O5 CLUSTER
+Macromolecule #30: PHEOPHYTIN A
+Macromolecule #31: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #32: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #33: BICARBONATE ION
+Macromolecule #34: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #35: HEME C
+Macromolecule #36: water
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 42.8 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 6.5 Component:
Details: 100mM MES pH6.5, 5mM CaCl2, 5% glycerol, 0.03% DDM | |||||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: The sample-on-grid was illuminated with one and two flashes of light. | |||||||||||||||
Details | highly purified monodisperse sample of dPSIIcc |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
---|---|
Output model | PDB-9evx: |