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Yorodumi- EMDB-9839: Structure of PSII-FCP supercomplex from a centric diatom Chaetoce... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9839 | |||||||||
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Title | Structure of PSII-FCP supercomplex from a centric diatom Chaetoceros gracilis at 3.02 angstrom resolution | |||||||||
Map data | PSII-FCP | |||||||||
Sample |
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Function / homology | Function and homology information photosystem II assembly / photosystem II stabilization / thylakoid / photosystem II / extrinsic component of membrane / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / respiratory electron transport chain ...photosystem II assembly / photosystem II stabilization / thylakoid / photosystem II / extrinsic component of membrane / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Chaetoceros gracilis (Diatom) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.02 Å | |||||||||
Authors | Pi X / Zhao S / Wang W / Kuang T / Sui S / Shen J | |||||||||
Citation | Journal: Science / Year: 2019 Title: The pigment-protein network of a diatom photosystem II-light-harvesting antenna supercomplex. Authors: Xiong Pi / Songhao Zhao / Wenda Wang / Desheng Liu / Caizhe Xu / Guangye Han / Tingyun Kuang / Sen-Fang Sui / Jian-Ren Shen / Abstract: Diatoms play important roles in global primary productivity and biogeochemical cycling of carbon, in part owing to the ability of their photosynthetic apparatus to adapt to rapidly changing light ...Diatoms play important roles in global primary productivity and biogeochemical cycling of carbon, in part owing to the ability of their photosynthetic apparatus to adapt to rapidly changing light intensity. We report a cryo-electron microscopy structure of the photosystem II (PSII)-fucoxanthin (Fx) chlorophyll (Chl) a/c binding protein (FCPII) supercomplex from the centric diatom The supercomplex comprises two protomers, each with two tetrameric and three monomeric FCPIIs around a PSII core that contains five extrinsic oxygen-evolving proteins at the lumenal surface. The structure reveals the arrangement of a huge pigment network that contributes to efficient light energy harvesting, transfer, and dissipation processes in the diatoms. | |||||||||
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_9839.map.gz | 138.7 MB | EMDB map data format | |
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Header (meta data) | emd-9839-v30.xml emd-9839.xml | 40 KB 40 KB | Display Display | EMDB header |
Images | emd_9839.png | 188.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9839 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9839 | HTTPS FTP |
-Validation report
Summary document | emd_9839_validation.pdf.gz | 582.7 KB | Display | EMDB validaton report |
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Full document | emd_9839_full_validation.pdf.gz | 582.3 KB | Display | |
Data in XML | emd_9839_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_9839_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9839 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9839 | HTTPS FTP |
-Related structure data
Related structure data | 6jluMC 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_9839.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PSII-FCP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.30654 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 : PSII-FCP supercomplex
+Supramolecule #1: PSII-FCP supercomplex
+Macromolecule #1: PsbA
+Macromolecule #2: PsbB
+Macromolecule #3: PsbC
+Macromolecule #4: PsbD
+Macromolecule #5: PsbE
+Macromolecule #6: PsbF
+Macromolecule #7: Psb31
+Macromolecule #8: Photosystem II reaction center protein H
+Macromolecule #9: PsbI
+Macromolecule #10: PsbJ
+Macromolecule #11: PsbK
+Macromolecule #12: PsbL
+Macromolecule #13: PsbM
+Macromolecule #14: Psb34
+Macromolecule #15: Extrinsic protein in photosystem II
+Macromolecule #16: FCP-D
+Macromolecule #17: Extrinsic protein in photosystem II
+Macromolecule #18: PsbG
+Macromolecule #19: PsbT
+Macromolecule #20: Extrinsic protein in photosystem II
+Macromolecule #21: Cytochrome c-550
+Macromolecule #22: PsbW
+Macromolecule #23: Photosystem II reaction center X protein
+Macromolecule #24: PsbY
+Macromolecule #25: PsbZ
+Macromolecule #26: FCP-E
+Macromolecule #27: FCP-A
+Macromolecule #28: FCP-F
+Macromolecule #29: CA-MN4-O5 CLUSTER
+Macromolecule #30: FE (II) ION
+Macromolecule #31: CHLOROPHYLL A
+Macromolecule #32: PHEOPHYTIN A
+Macromolecule #33: BETA-CAROTENE
+Macromolecule #34: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #35: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #36: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #37: BICARBONATE ION
+Macromolecule #38: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #39: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #40: CHLORIDE ION
+Macromolecule #41: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #42: Chlorophyll c1
+Macromolecule #43: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...
+Macromolecule #44: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...
+Macromolecule #45: Chlorophyll c2
+Macromolecule #46: water
-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: 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 42033 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |