+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15522 | ||||||||||||||||||
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Title | RCII/PSI complex, class 3 | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | photosystem / assembly factor / membrane protein / PHOTOSYNTHESIS | ||||||||||||||||||
Function / homology | Function and homology information plasma membrane-derived thylakoid photosystem II / plasma membrane-derived photosystem I / thylakoid lumen / photosystem II assembly / oxygen evolving activity / photosystem II / photosystem II reaction center / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I ...plasma membrane-derived thylakoid photosystem II / plasma membrane-derived photosystem I / thylakoid lumen / photosystem II assembly / oxygen evolving activity / photosystem II / photosystem II reaction center / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem I / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / heme binding / magnesium ion binding / identical protein binding / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Zhao Z / Vercellino I / Knoppova J / Sobotka R / Murray JW / Nixon PJ / Sazanov LA / Komenda J | ||||||||||||||||||
Funding support | United Kingdom, European Union, Czech Republic, 5 items
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Citation | Journal: Nat Commun / Year: 2023 Title: The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Authors: Ziyu Zhao / Irene Vercellino / Jana Knoppová / Roman Sobotka / James W Murray / Peter J Nixon / Leonid A Sazanov / Josef Komenda / Abstract: Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly ...Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising MnCaO cluster, thereby preventing the premature binding of Mn and Ca ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the MnCaO cluster. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15522.map.gz | 227.8 MB | EMDB map data format | |
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Header (meta data) | emd-15522-v30.xml emd-15522.xml | 50.5 KB 50.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15522_fsc.xml | 14.9 KB | Display | FSC data file |
Images | emd_15522.png | 92 KB | ||
Others | emd_15522_half_map_1.map.gz emd_15522_half_map_2.map.gz | 194 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15522 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15522 | HTTPS FTP |
-Related structure data
Related structure data | 8am5MC 8aslC 8aspC 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_15522.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.22 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map 1
File | emd_15522_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_15522_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RCII/PSI complex
+Supramolecule #1: RCII/PSI complex
+Macromolecule #1: Photosystem II protein D1 2
+Macromolecule #2: Photosystem II D2 protein
+Macromolecule #3: Cytochrome b559 subunit alpha
+Macromolecule #4: Cytochrome b559 subunit beta
+Macromolecule #5: Photosystem II reaction center protein I
+Macromolecule #6: Photosystem II assembly lipoprotein Ycf48
+Macromolecule #7: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #8: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #9: Photosystem I iron-sulfur center
+Macromolecule #10: Photosystem I reaction center subunit II
+Macromolecule #11: Photosystem I reaction center subunit IV
+Macromolecule #12: Photosystem I reaction center subunit III
+Macromolecule #13: Photosystem I reaction center subunit VIII
+Macromolecule #14: Photosystem I reaction center subunit IX
+Macromolecule #15: Photosystem I reaction center subunit PsaK 1
+Macromolecule #16: Photosystem I reaction center subunit XI
+Macromolecule #17: Photosystem I reaction center subunit XII
+Macromolecule #18: FE (II) ION
+Macromolecule #19: CHLOROPHYLL A
+Macromolecule #20: PHEOPHYTIN A
+Macromolecule #21: BETA-CAROTENE
+Macromolecule #22: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #23: CHLOROPHYLL A ISOMER
+Macromolecule #24: PHYLLOQUINONE
+Macromolecule #25: IRON/SULFUR CLUSTER
+Macromolecule #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #27: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #28: beta,beta-carotene-4,4'-dione
+Macromolecule #29: beta,beta-caroten-4-one
+Macromolecule #30: (3'R)-3'-hydroxy-beta,beta-caroten-4-one
+Macromolecule #31: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,...
+Macromolecule #32: DODECYL-BETA-D-MALTOSIDE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 6.5 |
Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 2853 / Average electron dose: 90.9 e/Å2 |
-Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: OTHER / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||
Output model | PDB-8am5: |