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Yorodumi- EMDB-37133: Cryo-EM structure of an intermediate-state complex during the pro... -
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-Basic information
Entry | Database: EMDB / ID: EMD-37133 | ||||||||||||
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Title | Cryo-EM structure of an intermediate-state complex during the process of photosystem II repair | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | monomeric Photosystem II / PSII repair / PHOTOSYNTHESIS | ||||||||||||
Function / homology | Function and homology information photosystem II repair / 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 / photosynthesis, light reaction ...photosystem II repair / 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 / photosynthesis, light reaction / chloroplast thylakoid membrane / phosphate ion binding / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||||||||
Authors | Li A / Wang Y / Liu Z | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis for an early stage of the photosystem II repair cycle in Chlamydomonas reinhardtii. Authors: Anjie Li / Tingting You / Xiaojie Pang / Yidi Wang / Lijin Tian / Xiaobo Li / Zhenfeng Liu / Abstract: Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs ...Photosystem II (PSII) catalyzes water oxidation and plastoquinone reduction by utilizing light energy. It is highly susceptible to photodamage under high-light conditions and the damaged PSII needs to be restored through a process known as the PSII repair cycle. The detailed molecular mechanism underlying the PSII repair process remains mostly elusive. Here, we report biochemical and structural features of a PSII-repair intermediate complex, likely arrested at an early stage of the PSII repair process in the green alga Chlamydomonas reinhardtii. The complex contains three protein factors associated with a damaged PSII core, namely Thylakoid Enriched Factor 14 (TEF14), Photosystem II Repair Factor 1 (PRF1), and Photosystem II Repair Factor 2 (PRF2). TEF14, PRF1 and PRF2 may facilitate the release of the manganese-stabilizing protein PsbO, disassembly of peripheral light-harvesting complexes from PSII and blockage of the Q site, respectively. Moreover, an α-tocopherol quinone molecule is located adjacent to the heme group of cytochrome b, potentially fulfilling a photoprotective role by preventing the generation of reactive oxygen species. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37133.map.gz | 112.9 MB | EMDB map data format | |
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Header (meta data) | emd-37133-v30.xml emd-37133.xml | 32.3 KB 32.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37133_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_37133.png | 142.7 KB | ||
Filedesc metadata | emd-37133.cif.gz | 8.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37133 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37133 | HTTPS FTP |
-Validation report
Summary document | emd_37133_validation.pdf.gz | 476.9 KB | Display | EMDB validaton report |
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Full document | emd_37133_full_validation.pdf.gz | 476.5 KB | Display | |
Data in XML | emd_37133_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_37133_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37133 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37133 | HTTPS FTP |
-Related structure data
Related structure data | 8kdeMC 8zeeC C: citing same article (ref.) M: atomic model generated by this map |
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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_37133.map.gz / Format: CCP4 / Size: 125 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: 1.04 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Cryo-EM structure of an intermediate-state complex during the pro...
+Supramolecule #1: Cryo-EM structure of an intermediate-state complex during the pro...
+Macromolecule #1: Photosystem II CP47 reaction center protein
+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 H
+Macromolecule #6: Photosystem II reaction center protein I
+Macromolecule #7: Photosystem II reaction center protein K
+Macromolecule #8: Photosystem II reaction center protein L
+Macromolecule #9: Photosystem II reaction center protein M
+Macromolecule #10: Photosystem II reaction center protein T
+Macromolecule #11: Photosystem II reaction center protein Ycf12
+Macromolecule #12: Uncharacterized protein
+Macromolecule #13: Photosystem II reaction center protein Z
+Macromolecule #14: Thylakoid enriched factor 14 (TEF14)
+Macromolecule #15: Photosystem II repair factor 1 (PRF1)
+Macromolecule #16: Photosystem II CP43 reaction center protein
+Macromolecule #17: Photosystem II protein D1
+Macromolecule #18: Photosystem II repair factor 2 (PRF2)
+Macromolecule #19: CHLOROPHYLL A
+Macromolecule #20: BETA-CAROTENE
+Macromolecule #21: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #22: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #23: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #24: PHEOPHYTIN A
+Macromolecule #25: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #26: RRR-ALPHA-TOCOPHERYLQUINONE
+Macromolecule #27: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #28: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #29: BICARBONATE ION
+Macromolecule #30: FE (II) ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 |
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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 K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 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: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |