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- EMDB-37442: FCP pentamer in Chaetoceros gracilis -

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Basic information

Entry
Database: EMDB / ID: EMD-37442
TitleFCP pentamer in Chaetoceros gracilis
Map data
Sample
  • Complex: FCP pentamer in Chaetoceros gracilis
    • Protein or peptide: Chlorophyll a/c-binding protein Lhcf6
    • Protein or peptide: Fucoxanthin-chlorophyll a/c protein
    • Protein or peptide: Chlorophyll a/b-binding protein
    • Protein or peptide: Chlorophyll a/c-binding protein Lhcf7
  • Ligand: (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
  • Ligand: CHLOROPHYLL A
  • Ligand: Chlorophyll c2
  • Ligand: Chlorophyll c1
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
KeywordsFCP pentamer in Chaetoceros gracilis / PHOTOSYNTHESIS
Biological speciesChaetoceros neogracilis (Diatom)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsFeng Y / Li Z / Zhou C / Liu C / Shen J-R / Wang W
Funding support China, 1 items
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, 2023-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37442.png

Downloads & links

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Map

FileDownload / File: emd_37442.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 480 pix.
= 499.2 Å		1.04 Å/pix.
x 480 pix.
= 499.2 Å		1.04 Å/pix.
x 480 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-0.52565366 - 1.18676
Average (Standard dev.)-0.00038450657 (±0.013717871)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 499.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37442_half_map_1.map
Projections & Slices
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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_37442_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : FCP pentamer in Chaetoceros gracilis

EntireName: FCP pentamer in Chaetoceros gracilis
Components
  • Complex: FCP pentamer in Chaetoceros gracilis
    • Protein or peptide: Chlorophyll a/c-binding protein Lhcf6
    • Protein or peptide: Fucoxanthin-chlorophyll a/c protein
    • Protein or peptide: Chlorophyll a/b-binding protein
    • Protein or peptide: Chlorophyll a/c-binding protein Lhcf7
  • Ligand: (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
  • Ligand: CHLOROPHYLL A
  • Ligand: Chlorophyll c2
  • Ligand: Chlorophyll c1
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Supramolecule #1: FCP pentamer in Chaetoceros gracilis

SupramoleculeName: FCP pentamer in Chaetoceros gracilis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2, #4
Source (natural)Organism: Chaetoceros neogracilis (Diatom)

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Macromolecule #1: Chlorophyll a/c-binding protein Lhcf6

MacromoleculeName: Chlorophyll a/c-binding protein Lhcf6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros neogracilis (Diatom)
Molecular weightTheoretical: 22.75874 KDa
SequenceString: MMKTAILAAM LGSAAAFVPA QQSKVSTSLA ASELEDGIGA VAPLGYFDPL GYIKDEETFI RYRAVERKHG RVAMMAMLGT FVHNNGWTF DGYLSPSQGL KFSDIDSGIG GLFQVPPAGL AQIILLCGFV ELAWWPASNL SGDYGVRLGT LNDWEEQPAK Y YRQKNAEL ...String:
MMKTAILAAM LGSAAAFVPA QQSKVSTSLA ASELEDGIGA VAPLGYFDPL GYIKDEETFI RYRAVERKHG RVAMMAMLGT FVHNNGWTF DGYLSPSQGL KFSDIDSGIG GLFQVPPAGL AQIILLCGFV ELAWWPASNL SGDYGVRLGT LNDWEEQPAK Y YRQKNAEL NNGRAAMMGI LGTFTHEVIT GQNFAEQAAA GHFSPFGDGQ GFF

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Macromolecule #2: Chlorophyll a/b-binding protein

MacromoleculeName: Chlorophyll a/b-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros neogracilis (Diatom)
Molecular weightTheoretical: 22.098182 KDa
SequenceString: MKLAVAALLV ASAAAFAPAP ASKASTSLKV SEIELGVTEP LGVYDPLGWL ESEPEAFERR RAVERKHGRV AMAAVVGTIV HNNHIVFDG YLSPSNNLKF SDIPTGVDGI RAIPTAGLAQ ILAFFALVEL AWMPASKYDG DYGVGYFGTD IKDPEEKARK L NVELNNGR ...String:
MKLAVAALLV ASAAAFAPAP ASKASTSLKV SEIELGVTEP LGVYDPLGWL ESEPEAFERR RAVERKHGRV AMAAVVGTIV HNNHIVFDG YLSPSNNLKF SDIPTGVDGI RAIPTAGLAQ ILAFFALVEL AWMPASKYDG DYGVGYFGTD IKDPEEKARK L NVELNNGR AAMMGIMGNM VAEVLTGQTM YEQYASGHIS PFGDGQGVF

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Macromolecule #3: Fucoxanthin-chlorophyll a/c protein

MacromoleculeName: Fucoxanthin-chlorophyll a/c protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros neogracilis (Diatom)
Molecular weightTheoretical: 21.143453 KDa
SequenceString: MKLALLASLV ASAAAFAPSK VAQTSTALKA FENELGAQPP LGFFDPLGLV EDGNQAKFDR LRYVELKHGR ISMLAVVGYL IEKAGIRLP GNISYDGTSF ADIPDGFAAL SKIPDAGLFQ LFAFIGFLEV FVMKDITGGE FVGDFRNGFI DFGWDSFDEE T KLKKRAIE ...String:
MKLALLASLV ASAAAFAPSK VAQTSTALKA FENELGAQPP LGFFDPLGLV EDGNQAKFDR LRYVELKHGR ISMLAVVGYL IEKAGIRLP GNISYDGTSF ADIPDGFAAL SKIPDAGLFQ LFAFIGFLEV FVMKDITGGE FVGDFRNGFI DFGWDSFDEE T KLKKRAIE LNQGRAAMMG ILALMVHEKL GVSLLPQ

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Macromolecule #4: Chlorophyll a/c-binding protein Lhcf7

MacromoleculeName: Chlorophyll a/c-binding protein Lhcf7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros neogracilis (Diatom)
Molecular weightTheoretical: 22.298115 KDa
SequenceString: MKLAIAALLA TSAAAFTTSP ASRATTSLQV SEIELGATEP LGVFDPLGWL ETEPEAFERR RAVERKHGRV AMAAVVGTIV HNNHIVFDG YISPSNNLKF SDIPTGIDGI FSVPTAGLAQ IIAFLGFVEL AWLPASQYDG DYGVGYFGND ILDPEEKARK L NAELNNGR ...String:
MKLAIAALLA TSAAAFTTSP ASRATTSLQV SEIELGATEP LGVFDPLGWL ETEPEAFERR RAVERKHGRV AMAAVVGTIV HNNHIVFDG YISPSNNLKF SDIPTGIDGI FSVPTAGLAQ IIAFLGFVEL AWLPASQYDG DYGVGYFGND ILDPEEKARK L NAELNNGR AAMMGIMGNM VAEKITGQTM YEQYAAGHFN PFNDGEGFF

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Macromolecule #5: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...

MacromoleculeName: (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: 5 / Number of copies: 30 / Formula: A86
Molecular weightTheoretical: 658.906 Da

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Macromolecule #6: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 6 / Number of copies: 29 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #7: Chlorophyll c2

MacromoleculeName: Chlorophyll c2 / type: ligand / ID: 7 / Number of copies: 9 / Formula: KC2
Molecular weightTheoretical: 608.926 Da
Chemical component information

ChemComp-KC2:
Chlorophyll c2

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Macromolecule #8: Chlorophyll c1

MacromoleculeName: Chlorophyll c1 / type: ligand / ID: 8 / Number of copies: 9 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1

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Macromolecule #9: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 9 / Number of copies: 5 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #10: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 10 / Number of copies: 2 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 681510
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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