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Yorodumi- EMDB-18848: Cryo-EM Structure of native Photosystem II assembly intermediate ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18848 | |||||||||
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Title | Cryo-EM Structure of native Photosystem II assembly intermediate fromChlamydomonas reinhardtii | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Photosystem II / photosynthesis / biogenesis of PSII / assembly intermediate / CryoEM / assembly factor / Chlamydomonas reinhardtii | |||||||||
Function / homology | Function and homology information photosystem II repair / chloroplast thylakoid lumen / photosystem II assembly / oxygen evolving activity / 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 repair / chloroplast thylakoid lumen / photosystem II assembly / oxygen evolving activity / 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 / photosynthetic electron transport in photosystem II / chlorophyll binding / chloroplast thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Fadeeva M / Klaiman D / Kandiah E / Nelson N | |||||||||
Funding support | Israel, 1 items
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Citation | Journal: Front Plant Sci / Year: 2023 Title: Structure of native photosystem II assembly intermediate from . Authors: Mariia Fadeeva / Daniel Klaiman / Eaazhisai Kandiah / Nathan Nelson / Abstract: Photosystem II (PSII) is a dimer consisting of at least 13 nuclear-encoded and four chloroplast-encoded protein subunits that collectively function as a sunlight-driven oxidoreductase. In this ... Photosystem II (PSII) is a dimer consisting of at least 13 nuclear-encoded and four chloroplast-encoded protein subunits that collectively function as a sunlight-driven oxidoreductase. In this study, we present the inaugural structure of a green alga PSII assembly intermediate (pre-PSII-int). This intermediate was isolated from chloroplast membranes of the temperature-sensitive mutant TSP4, cultivated for 14 hours at a non-permissive temperature. The assembly state comprises a monomer containing subunits A, B, C, D, E, F, H, I, K, and two novel assembly factors, Psb1 and Psb2. Psb1 is identified as a novel transmembrane helix located adjacent to PsbE and PsbF (cytochrome b559). The absence of PsbJ, typically found in mature PSII close to this position, indicates that Psb1 functions as an assembly factor. Psb2 is an eukaryotic homolog of the cyanobacterial assembly factor Psb27. The presence of iron, coupled with the absence of Q, Q, and the manganese cluster, implies a protective mechanism against photodamage and provides insights into the intricate assembly process. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18848.map.gz | 137.8 MB | EMDB map data format | |
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Header (meta data) | emd-18848-v30.xml emd-18848.xml | 31.7 KB 31.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18848_fsc.xml | 12 KB | Display | FSC data file |
Images | emd_18848.png | 29.5 KB | ||
Filedesc metadata | emd-18848.cif.gz | 8 KB | ||
Others | emd_18848_half_map_1.map.gz emd_18848_half_map_2.map.gz | 118.1 MB 118.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18848 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18848 | HTTPS FTP |
-Related structure data
Related structure data | 8r2iMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18848.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_18848_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18848_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Photosystem II assembly intermediate from Chlamydomonas reinhardtii
+Supramolecule #1: Photosystem II assembly intermediate from Chlamydomonas reinhardtii
+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 K
+Macromolecule #10: Chain U, Predicted protein
+Macromolecule #11: Photosystem II reaction center protein Ycf12
+Macromolecule #12: FE (II) ION
+Macromolecule #13: CHLOROPHYLL A
+Macromolecule #14: PHEOPHYTIN A
+Macromolecule #15: BETA-CAROTENE
+Macromolecule #16: octyl beta-D-glucopyranoside
+Macromolecule #17: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #18: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #19: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #20: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #21: BICARBONATE ION
+Macromolecule #22: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #23: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #24: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 6 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 25758 / Average exposure time: 1.8 sec. / Average electron dose: 1.07 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |