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- EMDB-35899: FCP heterodimer, Lhca2, and Lhcf5 together as the M1 side binds t... -

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Basic information

Entry
Database: EMDB / ID: EMD-35899
TitleFCP heterodimer, Lhca2, and Lhcf5 together as the M1 side binds to the PSII core in the diatom Thalassiosira pseudonana
Map data
Sample
  • Complex: M1 local refinement in the PSII-FCPII from the Thalassiosira pseudonana at 3.19 angstrom
    • Protein or peptide: x 4 types
  • Ligand: x 9 types
KeywordsFCP / heterodimer / 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 chl a/c protein, lhca clade / Fucoxanthin-chlorophyll a-c binding protein, plastid / Fucoxanthin chlorophyll a/c protein 6 / Fucoxanthin chlorophyll a/c protein 5
Similarity search - Component
Biological speciesThalassiosira pseudonana (Diatom)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsLi Z / Feng Y / Wang W / Shen JR
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences2021YFA1300403 China
CitationJournal: Sci Adv / Year: 2023
Title: Structure of a diatom photosystem II supercomplex containing a member of Lhcx family and dimeric FCPII.
Authors: Yue Feng / Zhenhua Li / Xiaoyi Li / Lili Shen / Xueyang Liu / Cuicui Zhou / Jinyang Zhang / Min Sang / Guangye Han / Wenqiang Yang / Tingyun Kuang / Wenda Wang / Jian-Ren Shen /
Abstract: Diatoms rely on fucoxanthin chlorophyll -binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We ...Diatoms rely on fucoxanthin chlorophyll -binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We report a unique structure of photosystem II (PSII)-FCPII supercomplex from at 2.68-Å resolution by cryo-electron microscopy. FCPIIs within this PSII-FCPII supercomplex exist in dimers and monomers, and a homodimer and a heterodimer were found to bind to a PSII core. The FCPII homodimer is formed by Lhcf7 and associates with PSII through an Lhcx family antenna Lhcx6_1, whereas the heterodimer is formed by Lhcf6 and Lhcf11 and connects to the core together with an Lhcf5 monomer through Lhca2 monomer. An extended pigment network consisting of diatoxanthins, diadinoxanthins, fucoxanthins, and chlorophylls is revealed, which functions in efficient light harvesting, energy transfer, and dissipation. These results provide a structural basis for revealing the energy transfer and dissipation mechanisms and also for the structural diversity of FCP antennas in diatoms.
History
DepositionApr 10, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35899.png

Downloads & links

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Map

FileDownload / File: emd_35899.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.24929167 - 0.5981119
Average (Standard dev.)-0.0006765118 (±0.009176806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35899_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_35899_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 : M1 local refinement in the PSII-FCPII from the Thalassiosira pseu...

EntireName: M1 local refinement in the PSII-FCPII from the Thalassiosira pseudonana at 3.19 angstrom
Components
  • Complex: M1 local refinement in the PSII-FCPII from the Thalassiosira pseudonana at 3.19 angstrom
    • Protein or peptide: Fucoxanthin chl a/c protein, lhca clade
    • Protein or peptide: Fucoxanthin-chlorophyll a-c binding protein, plastid
    • Protein or peptide: Fucoxanthin chlorophyll a/c protein 6
    • Protein or peptide: Fucoxanthin chlorophyll a/c protein 5
  • Ligand: CHLOROPHYLL A
  • Ligand: Chlorophyll c1
  • 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: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: Chlorophyll c2
  • Ligand: DODECYL-BETA-D-MALTOSIDE

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Supramolecule #1: M1 local refinement in the PSII-FCPII from the Thalassiosira pseu...

SupramoleculeName: M1 local refinement in the PSII-FCPII from the Thalassiosira pseudonana at 3.19 angstrom
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Thalassiosira pseudonana (Diatom)

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Macromolecule #1: Fucoxanthin chl a/c protein, lhca clade

MacromoleculeName: Fucoxanthin chl a/c protein, lhca clade / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana (Diatom)
Molecular weightTheoretical: 24.10099 KDa
SequenceString: WNEAPRALPF GSAPPTLDGS LVGDVGFDPI GFSTAPFASF NNPIYQEGNF MTDVQWLREA ELTHGRIAQL AVVGFIWPAL FGTFPGNEN FGGADAYSYV NPLEAINHIP SLAIYQIVGG MAWVEYQRVQ RIKEQGKDRI SGDIGLAYPG GWNPFNINYS P EEYAEKQL ...String:
WNEAPRALPF GSAPPTLDGS LVGDVGFDPI GFSTAPFASF NNPIYQEGNF MTDVQWLREA ELTHGRIAQL AVVGFIWPAL FGTFPGNEN FGGADAYSYV NPLEAINHIP SLAIYQIVGG MAWVEYQRVQ RIKEQGKDRI SGDIGLAYPG GWNPFNINYS P EEYAEKQL QEIKHCRLAM LGAFGLFFQA LNSGEDIVSQ LSPAFAAPEY AAKAGYFLPQ GI

UniProtKB: Fucoxanthin chl a/c protein, lhca clade

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Macromolecule #2: Fucoxanthin-chlorophyll a-c binding protein, plastid

MacromoleculeName: Fucoxanthin-chlorophyll a-c binding protein, plastid / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana (Diatom)
Molecular weightTheoretical: 17.7451 KDa
SequenceString:
ENEIGVLPPT GFFDPAGLSD GISQEKFDSY RLAELKHGRA AMLAVLGYVA PETYRFGYDL IPGELSTNDI PNGVAAIKAI PFGGWAQMI AFVGCVETYG WFTSPTGVLD LPDDILAKRQ TAELQHGRLA MLAFLELIRH DSQNLAQPGF DGLDNLITGL P FLY

UniProtKB: Fucoxanthin-chlorophyll a-c binding protein, plastid

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Macromolecule #3: Fucoxanthin chlorophyll a/c protein 6

MacromoleculeName: Fucoxanthin chlorophyll a/c protein 6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana (Diatom)
Molecular weightTheoretical: 17.614867 KDa
SequenceString:
ESEIGAQAPL GFWDPLGFLD RADQETFDRL RYVELKHGRI AQLAFVGNLI TRAGYHLPGD ISLGRAFADV PNGIAAINGP DAISTAALL QTLAFIGFLE TRVMIDATGE SQFRGDFRNG FDFGWDKQSP EWQTNKRAIE LNQGRAAMMG ILGLMMHEQV G

UniProtKB: Fucoxanthin chlorophyll a/c protein 6

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Macromolecule #4: Fucoxanthin chlorophyll a/c protein 5

MacromoleculeName: Fucoxanthin chlorophyll a/c protein 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana (Diatom)
Molecular weightTheoretical: 18.380953 KDa
SequenceString:
FENELGAQPP LGFFDPLGML DEAGQARFDR LRYVELKHGR ICQLAFLGNI ITRAGIHLPG AISLDGTKFS DIGNGWAGSF EVPKDGALQ ILFFVGFLEL FVMKDVTGEG EFVGDFRNGA LDFGWDSFSE ETKLQKRAIE LNNGRAAMMG ILGLMVHEQL G GELPIVGQ

UniProtKB: Fucoxanthin chlorophyll a/c protein 5

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Macromolecule #5: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 5 / Number of copies: 39 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #6: Chlorophyll c1

MacromoleculeName: Chlorophyll c1 / type: ligand / ID: 6 / Number of copies: 3 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1

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Macromolecule #7: (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: 7 / Number of copies: 17 / Formula: A86
Molecular weightTheoretical: 658.906 Da

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Macromolecule #8: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...

MacromoleculeName: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
type: ligand / ID: 8 / Number of copies: 2 / Formula: DD6
Molecular weightTheoretical: 582.855 Da
Chemical component information

ChemComp-DD6:
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol

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Macromolecule #9: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 9 / 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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Macromolecule #10: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 10 / Number of copies: 4 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #11: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 11 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #12: Chlorophyll c2

MacromoleculeName: Chlorophyll c2 / type: ligand / ID: 12 / Number of copies: 3 / Formula: KC2
Molecular weightTheoretical: 608.926 Da
Chemical component information

ChemComp-KC2:
Chlorophyll c2

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Macromolecule #13: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 13 / Number of copies: 2 / 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 BIOQUANTUM (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: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97098
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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