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- EMDB-36466: FCP trimer in diatom Thalassiosira pseudonana -

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Basic information

Entry
Database: EMDB / ID: EMD-36466
TitleFCP trimer in diatom Thalassiosira pseudonana
Map data
Sample
  • Complex: FCP trimer
    • Protein or peptide: Fucoxanthin chlorophyll a/c protein 8
  • 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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
KeywordsFCP trimer / PHOTOSYNTHESIS
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
Fucoxanthin chlorophyll a/c protein 8
Similarity search - Component
Biological speciesThalassiosira pseudonana CCMP1335 (Diatom)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsFeng Y / Li Z / Zhou CC / Liu C / Shen JR / Wang W
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences31970260 China
CitationJournal: To Be Published
Title: FCP trimer in diatom Thalassiosira pseudonana
Authors: Feng Y / Li Z / Zhou CC / Wang W / Shen JR
History
DepositionJun 10, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36466.png

Downloads & links

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Map

FileDownload / File: emd_36466.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.253
Minimum - Maximum-0.29004186 - 0.77496815
Average (Standard dev.)0.0020734544 (±0.021739319)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_36466_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36466_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36466_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FCP trimer

EntireName: FCP trimer
Components
  • Complex: FCP trimer
    • Protein or peptide: Fucoxanthin chlorophyll a/c protein 8
  • 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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Supramolecule #1: FCP trimer

SupramoleculeName: FCP trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)

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Macromolecule #1: Fucoxanthin chlorophyll a/c protein 8

MacromoleculeName: Fucoxanthin chlorophyll a/c protein 8 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana CCMP1335 (Diatom)
Molecular weightTheoretical: 19.652232 KDa
SequenceString:
AFEDELGAQA PLGFFDPFGM LSGDCTQERF DRLRYVEIKH GRIAQLAFLG QVVTRAGIHL PGSINYAGDS FDSFPNGVAA LFGPNSIPT AGLVQIISFI GILECAFMRD VPGTGNEHVG DFRNGYIDFG WDEFDEETKL SKRAIELNNG RAAMMGILGL M VHEEIIPL GYDADLPIIG HL

UniProtKB: Fucoxanthin chlorophyll a/c protein 8

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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: 21 / 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: 6 / 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: 3 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1

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Macromolecule #6: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 6 / Number of copies: 3 / 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: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103596
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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