+Open data
-Basic information
Entry | Database: PDB / ID: 8wcl | ||||||
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Title | FCP pentamer in Chaetoceros gracilis | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / FCP pentamer in Chaetoceros gracilis | ||||||
Function / homology | Chem-A86 / CHLOROPHYLL A / Chlorophyll c1 / Chlorophyll c2 / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE Function and homology information | ||||||
Biological species | Chaetoceros neogracilis (Diatom) | ||||||
Method | ELECTRON MICROSCOPY / 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, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wcl.cif.gz | 251.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wcl.ent.gz | 219.6 KB | Display | PDB format |
PDBx/mmJSON format | 8wcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/8wcl ftp://data.pdbj.org/pub/pdb/validation_reports/wc/8wcl | HTTPS FTP |
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-Related structure data
Related structure data | 37442MC 8jp3C 8wckC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Chlorophyll a/c-binding protein ... , 2 types, 2 molecules 67
#1: Protein | Mass: 22758.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros neogracilis (Diatom) |
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#4: Protein | Mass: 22298.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros neogracilis (Diatom) |
-Protein , 2 types, 3 molecules 859
#2: Protein | Mass: 22098.182 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chaetoceros neogracilis (Diatom) #3: Protein | | Mass: 21143.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros neogracilis (Diatom) |
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-Sugars , 1 types, 5 molecules
#9: Sugar | ChemComp-LMT / |
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-Non-polymers , 5 types, 79 molecules
#5: Chemical | ChemComp-A86 / ( #6: Chemical | ChemComp-CLA / #7: Chemical | ChemComp-KC2 / #8: Chemical | ChemComp-KC1 / #10: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: FCP pentamer in Chaetoceros gracilis / Type: COMPLEX / Entity ID: #1, #3, #2, #4 / Source: NATURAL |
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Source (natural) | Organism: Chaetoceros neogracilis (Diatom) |
Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 681510 / Symmetry type: POINT | ||||||||||||||||||||||||
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