+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, contribute significantly to global primary productivity. Their substantial biomass is linked to enhanced absorption of blue-green light underwater, ...Diatoms, a group of prevalent marine algae, contribute significantly to global primary productivity. Their substantial biomass is linked to enhanced absorption of blue-green light underwater, facilitated by fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs), which exhibit oligomeric diversity across diatom species. Using mild clear native PAGE analysis of solubilized thylakoid membranes, we displayed monomeric, dimeric, trimeric, tetrameric, and pentameric FCPs in diatoms. Mass spectrometry analysis revealed that each oligomeric FCP has a specific protein composition, and together they constitute a large Lhcf family of FCP antennas. In addition, we resolved the structures of the Thalassiosira pseudonana FCP (Tp-FCP) homotrimer and the Chaetoceros gracilis FCP (Cg-FCP) pentamer by cryoelectron microscopy at 2.73-Å and 2.65-Å resolution, respectively. The distinct pigment compositions and organizations of various oligomeric FCPs affect their blue-green light-harvesting, excitation energy transfer pathways. Compared with dimeric and trimeric FCPs, the Cg-FCP tetramer and Cg-FCP pentamer exhibit stronger absorption by Chl c, redshifted and broader Chl a fluorescence emission, and more robust circular dichroism signals originating from Chl a-carotenoid dimers. These spectroscopic characteristics indicate that Chl a molecules in the Cg-FCP tetramer and Cg-FCP pentamer are more heterogeneous than in both dimers and the 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
Summary document | 8wcl_validation.pdf.gz | 5.1 MB | Display | wwPDB validaton report |
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Full document | 8wcl_full_validation.pdf.gz | 5.3 MB | Display | |
Data in XML | 8wcl_validation.xml.gz | 85.1 KB | Display | |
Data in CIF | 8wcl_validation.cif.gz | 102.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/8wcl ftp://data.pdbj.org/pub/pdb/validation_reports/wc/8wcl | HTTPS FTP |
-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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