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- EMDB-37441: FCP tetramer in Chaetoceros gracilis -

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Basic information

Entry
Database: EMDB / ID: EMD-37441
TitleFCP tetramer in Chaetoceros gracilis
Map data
Sample
  • Complex: FCP tetramer
    • Protein or peptide: Chlorophyll a/b-binding protein
  • 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
KeywordsFCP tetramers / PHOTOSYNTHESIS
Function / homologylight-harvesting complex / photosynthesis, light harvesting / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / plastid / chlorophyll binding / membrane / Chlorophyll a/b-binding protein
Function and homology information
Biological speciesChaetoceros neogracilis (Diatom)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsFeng Y / Li Z / Zhou C / Shen J-R / Liu C / 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, 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
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_37441.png

Downloads & links

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Map

FileDownload / File: emd_37441.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-0.37274167 - 1.174424
Average (Standard dev.)-0.00040824458 (±0.011222878)
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_37441_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_37441_half_map_2.map
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Sample components

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Entire : FCP tetramer

EntireName: FCP tetramer
Components
  • Complex: FCP tetramer
    • Protein or peptide: Chlorophyll a/b-binding protein
  • 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

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Supramolecule #1: FCP tetramer

SupramoleculeName: FCP tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chaetoceros neogracilis (Diatom)

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Macromolecule #1: Chlorophyll a/b-binding protein

MacromoleculeName: Chlorophyll a/b-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / 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

UniProtKB: Chlorophyll a/b-binding protein

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Macromolecule #2: (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: 2 / Number of copies: 24 / Formula: A86
Molecular weightTheoretical: 658.906 Da

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Macromolecule #3: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 24 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #4: Chlorophyll c2

MacromoleculeName: Chlorophyll c2 / type: ligand / ID: 4 / Number of copies: 8 / Formula: KC2
Molecular weightTheoretical: 608.926 Da
Chemical component information

ChemComp-KC2:
Chlorophyll c2

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Macromolecule #5: Chlorophyll c1

MacromoleculeName: Chlorophyll c1 / type: ligand / ID: 5 / Number of copies: 8 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1

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Macromolecule #6: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 6 / Number of copies: 8 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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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: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 946436
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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