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- PDB-8wck: FCP tetramer in Chaetoceros gracilis -

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Basic information

Entry
Database: PDB / ID: 8wck
TitleFCP tetramer in Chaetoceros gracilis
ComponentsChlorophyll a/b-binding protein
KeywordsPHOTOSYNTHESIS / FCP tetramers
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
Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein
Similarity search - Domain/homology
Chem-A86 / CHLOROPHYLL A / Chlorophyll c1 / Chlorophyll c2 / Chlorophyll a/b-binding protein
Similarity search - Component
Biological speciesChaetoceros neogracilis (Diatom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsFeng, Y. / Li, Z. / Zhou, C. / Shen, J.-R. / Liu, C. / Wang, W.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences2021YFA1300403 China
CitationJournal: 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
DepositionSep 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Chlorophyll a/b-binding protein
2: Chlorophyll a/b-binding protein
3: Chlorophyll a/b-binding protein
4: Chlorophyll a/b-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,49476
Polymers88,3934
Non-polymers51,10172
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein / Sugars , 2 types, 12 molecules 1234

#1: Protein
Chlorophyll a/b-binding protein


Mass: 22098.182 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chaetoceros neogracilis (Diatom) / References: UniProt: A0A679BXP6
#6: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 4 types, 64 molecules

#2: Chemical...
ChemComp-A86 / (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 / Fucoxanthin


Mass: 658.906 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C42H58O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C35H28MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-KC1 / Chlorophyll c1


Mass: 610.941 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C35H30MgN4O5 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FCP tetramer / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Chaetoceros neogracilis (Diatom)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 946436 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0089108
ELECTRON MICROSCOPYf_angle_d1.47513004
ELECTRON MICROSCOPYf_dihedral_angle_d13.3472684
ELECTRON MICROSCOPYf_chiral_restr0.0561088
ELECTRON MICROSCOPYf_plane_restr0.0041608

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