+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31905 | |||||||||
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Title | Structure of C2S2M2-type PSII-FCPII supercomplex from diatom | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information light-harvesting complex / : / photosynthesis, light harvesting in photosystem I / photosystem II assembly / photosystem II stabilization / photosystem II reaction center / thylakoid / photosynthetic electron transport chain / response to herbicide / plastid ...light-harvesting complex / : / photosynthesis, light harvesting in photosystem I / photosystem II assembly / photosystem II stabilization / photosystem II reaction center / thylakoid / photosynthetic electron transport chain / response to herbicide / plastid / extrinsic component of membrane / 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 / response to light stimulus / photosynthesis / respiratory electron transport chain / membrane => GO:0016020 / electron transfer activity / protein stabilization / iron ion binding / heme binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Chaetoceros gracilis (Diatom) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Nagao R / Kato K / Akita F / Miyazaki N / Shen JR | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex Authors: Nagao R / Kato K / Kumazawa M / Ifuku K / Yokono M / Suzuki T / Dohmae N / Akita F / Akimoto S / Miyazaki N / Shen JR | |||||||||
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_31905.map.gz | 38.1 MB | EMDB map data format | |
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Header (meta data) | emd-31905-v30.xml emd-31905.xml | 48.2 KB 48.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31905_fsc.xml | 17.9 KB | Display | FSC data file |
Images | emd_31905.png | 134.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31905 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31905 | HTTPS FTP |
-Validation report
Summary document | emd_31905_validation.pdf.gz | 366 KB | Display | EMDB validaton report |
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Full document | emd_31905_full_validation.pdf.gz | 365.6 KB | Display | |
Data in XML | emd_31905_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | emd_31905_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31905 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31905 | HTTPS FTP |
-Related structure data
Related structure data | 7vd5MC 7vd6C 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_31905.map.gz / Format: CCP4 / Size: 512 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: 1.113 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : C2S2M2-type PSII-FCPII supercomplex
+Supramolecule #1: C2S2M2-type PSII-FCPII supercomplex
+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 J
+Macromolecule #10: Photosystem II reaction center protein K
+Macromolecule #11: Photosystem II reaction center protein L
+Macromolecule #12: Photosystem II subunit
+Macromolecule #13: Extrinsic protein in photosystem II
+Macromolecule #14: Photosystem II reaction center protein T
+Macromolecule #15: Extrinsic protein in photosystem II
+Macromolecule #16: Cytochrome c-550
+Macromolecule #17: Photosystem II reaction center protein Ycf12
+Macromolecule #18: Photosystem II reaction center X protein
+Macromolecule #19: Photosystem II reaction center protein Z
+Macromolecule #20: Extrinsic protein in photosystem II
+Macromolecule #21: Photosystem II reaction center protein W
+Macromolecule #22: Unknown protein 0
+Macromolecule #23: Unknown protein 1
+Macromolecule #24: Chlorophyll a/b-binding protein
+Macromolecule #25: Fcpb2, Fucoxanthin chlorophyll a/c-binding protein
+Macromolecule #26: Chlorophyll a/b-binding protein
+Macromolecule #27: Chlorophyll a/b-binding protein
+Macromolecule #28: Chlorophyll a/b-binding protein
+Macromolecule #29: Fcpb3, Fucoxanthin chlorophyll a/c-binding protein
+Macromolecule #30: Fcpb4, Fucoxanthin chlorophyll a/c-binding protein
+Macromolecule #31: Chlorophyll a/b-binding protein
+Macromolecule #32: Fcpb5, Fucoxanthin chlorophyll a/c-binding protein
+Macromolecule #33: Fcpb6, Fucoxanthin chlorophyll a/c-binding protein
+Macromolecule #34: Fcpb7, Fucoxanthin chlorophyll a/c-binding protein
+Macromolecule #35: CA-MN4-O5 CLUSTER
+Macromolecule #36: FE (II) ION
+Macromolecule #37: CHLOROPHYLL A
+Macromolecule #38: PHEOPHYTIN A
+Macromolecule #39: BETA-CAROTENE
+Macromolecule #40: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #41: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #42: BICARBONATE ION
+Macromolecule #43: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #44: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #45: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #46: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #47: Chlorophyll c1
+Macromolecule #48: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...
+Macromolecule #49: UNKNOWN LIGAND
+Macromolecule #50: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...
+Macromolecule #51: DODECYL-ALPHA-D-MALTOSIDE
+Macromolecule #52: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.256 mg/mL | ||||||
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Buffer | pH: 6.5 / Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 20.0 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 |