+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37442 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | FCP pentamer in Chaetoceros gracilis | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | FCP pentamer in Chaetoceros gracilis / PHOTOSYNTHESIS | |||||||||
Biological species | Chaetoceros neogracilis (Diatom) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.65 Å | |||||||||
Authors | Feng Y / Li Z / Zhou C / Liu C / Shen J-R / Wang W | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: Plant Commun / Year: 2024 Title: Structural and spectroscopic insights into fucoxanthin chlorophyll a/c-binding proteins of diatoms in diverse oligomeric states. Authors: Cuicui Zhou / Yue Feng / Zhenhua Li / Lili Shen / Xiaoyi Li / Yumei Wang / Guangye Han / Tingyun Kuang / Cheng Liu / Jian-Ren Shen / Wenda Wang / Abstract: Diatoms, a group of prevalent marine algae, significantly contribute to global primary productivity. Their substantial biomass is linked to enhanced absorption of blue-green light underwater, ...Diatoms, a group of prevalent marine algae, significantly contribute to global primary productivity. Their substantial biomass is linked to enhanced absorption of blue-green light underwater, facilitated by fucoxanthin chlorophyll a/c-binding proteins (FCPs), exhibiting oligomeric diversity across diatom species. Utilizing mild CN-PAGE analysis on solubilized thylakoid membranes, we displayed monomeric, dimeric, trimeric, tetrameric and pentameric FCPs in diatoms. Mass spectrometry analysis revealed each oligomeric FCP has specific protein compositions, constituting a large Lhcf family of FCP antennas. In addition, we resolved the structures of Thalassiosira pseudonana FCP (Tp-FCP) homotrimer and Chaetoceros gracilis FCP (Cg-FCP) pentamer by cryo-electron microscopy at 2.73 Å and 2.65 Å resolutions, respectively. The distinct pigment composition and organization in various oligomeric FCPs change their blue-green light-harvesting, excitation energy transfer pathways. In comparison to dimeric and trimeric FCPs, Cg-FCP tetramer and Cg-FCP pentamer exhibit stronger absorption by Chls c, red-shifted and broader Chl a fluorescence emission, as well as more robust circular dichroism signals originating from Chl a-carotenoid dimers. These spectroscopic characteristics indicate that Chl a molecules in Cg-FCP tetramer and Cg-FCP pentamer are more heterogeneous than in both dimers and Tp-FCP trimer. The structural and spectroscopic insights provided by this study contribute to a better understanding of the mechanisms that empower diatoms to adapt to fluctuating light environments. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_37442.map.gz | 212.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-37442-v30.xml emd-37442.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37442_fsc.xml | 15.7 KB | Display | FSC data file |
Images | emd_37442.png | 106.8 KB | ||
Filedesc metadata | emd-37442.cif.gz | 5.8 KB | ||
Others | emd_37442_half_map_1.map.gz emd_37442_half_map_2.map.gz | 391.5 MB 391.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37442 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37442 | HTTPS FTP |
-Validation report
Summary document | emd_37442_validation.pdf.gz | 740.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_37442_full_validation.pdf.gz | 740 KB | Display | |
Data in XML | emd_37442_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | emd_37442_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37442 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37442 | HTTPS FTP |
-Related structure data
Related structure data | 8wclMC 8jp3C 8wckC M: atomic model generated by this map C: citing same article (ref.) |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_37442.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_37442_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_37442_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : FCP pentamer in Chaetoceros gracilis
+Supramolecule #1: FCP pentamer in Chaetoceros gracilis
+Macromolecule #1: Chlorophyll a/c-binding protein Lhcf6
+Macromolecule #2: Chlorophyll a/b-binding protein
+Macromolecule #3: Fucoxanthin-chlorophyll a/c protein
+Macromolecule #4: Chlorophyll a/c-binding protein Lhcf7
+Macromolecule #5: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...
+Macromolecule #6: CHLOROPHYLL A
+Macromolecule #7: Chlorophyll c2
+Macromolecule #8: Chlorophyll c1
+Macromolecule #9: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #10: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k 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: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |