+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36466 | |||||||||
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Title | FCP trimer in diatom Thalassiosira pseudonana | |||||||||
Map data | ||||||||||
Sample |
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Keywords | FCP trimer / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information light-harvesting complex / photosynthesis, light harvesting in photosystem I / plastid / chlorophyll binding / response to light stimulus / membrane Similarity search - Function | |||||||||
Biological species | Thalassiosira pseudonana CCMP1335 (Diatom) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.73 Å | |||||||||
Authors | Feng Y / Li Z / Zhou CC / Liu C / Shen JR / Wang W | |||||||||
Funding support | China, 1 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36466.map.gz | 32.1 MB | EMDB map data format | |
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Header (meta data) | emd-36466-v30.xml emd-36466.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36466_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_36466.png | 109 KB | ||
Filedesc metadata | emd-36466.cif.gz | 5.3 KB | ||
Others | emd_36466_additional_1.map.gz emd_36466_half_map_1.map.gz emd_36466_half_map_2.map.gz | 59.8 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36466 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36466 | HTTPS FTP |
-Validation report
Summary document | emd_36466_validation.pdf.gz | 725.6 KB | Display | EMDB validaton report |
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Full document | emd_36466_full_validation.pdf.gz | 725.2 KB | Display | |
Data in XML | emd_36466_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_36466_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36466 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36466 | HTTPS FTP |
-Related structure data
Related structure data | 8jp3MC 8wckC 8wclC 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_36466.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
-Additional map: #1
File | emd_36466_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36466_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36466_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : FCP trimer
Entire | Name: FCP trimer |
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Components |
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-Supramolecule #1: FCP trimer
Supramolecule | Name: FCP trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Thalassiosira pseudonana CCMP1335 (Diatom) |
-Macromolecule #1: Fucoxanthin chlorophyll a/c protein 8
Macromolecule | Name: Fucoxanthin chlorophyll a/c protein 8 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Thalassiosira pseudonana CCMP1335 (Diatom) |
Molecular weight | Theoretical: 19.652232 KDa |
Sequence | String: AFEDELGAQA PLGFFDPFGM LSGDCTQERF DRLRYVEIKH GRIAQLAFLG QVVTRAGIHL PGSINYAGDS FDSFPNGVAA LFGPNSIPT AGLVQIISFI GILECAFMRD VPGTGNEHVG DFRNGYIDFG WDEFDEETKL SKRAIELNNG RAAMMGILGL M VHEEIIPL GYDADLPIIG HL UniProtKB: Fucoxanthin chlorophyll a/c protein 8 |
-Macromolecule #2: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...
Macromolecule | Name: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate type: ligand / ID: 2 / Number of copies: 21 / Formula: A86 |
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Molecular weight | Theoretical: 658.906 Da |
-Macromolecule #3: CHLOROPHYLL A
Macromolecule | Name: CHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 24 / Formula: CLA |
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Molecular weight | Theoretical: 893.489 Da |
Chemical component information | ChemComp-CLA: |
-Macromolecule #4: Chlorophyll c2
Macromolecule | Name: Chlorophyll c2 / type: ligand / ID: 4 / Number of copies: 6 / Formula: KC2 |
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Molecular weight | Theoretical: 608.926 Da |
Chemical component information | ChemComp-KC2: |
-Macromolecule #5: Chlorophyll c1
Macromolecule | Name: Chlorophyll c1 / type: ligand / ID: 5 / Number of copies: 3 / Formula: KC1 |
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Molecular weight | Theoretical: 610.941 Da |
Chemical component information | ChemComp-KC1: |
-Macromolecule #6: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
Macromolecule | Name: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 6 / Number of copies: 3 / Formula: LMG |
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Molecular weight | Theoretical: 787.158 Da |
Chemical component information | ChemComp-LMG: |
-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 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 |