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- EMDB-37267: Structure of PSII-FCPII-G/H complex in the PSII-FCPII supercomple... -

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Entry
Database: EMDB / ID: EMD-37267
TitleStructure of PSII-FCPII-G/H complex in the PSII-FCPII supercomplex from Cyclotella meneghiniana
Map data
Sample
  • Complex: Cm-PSII-FCPII-G/H
    • Protein or peptide: FCPII-G, Fucoxanthin chlorophyll a/c binding protein
    • Protein or peptide: FCPII-H2, Fucoxanthin chlorophyll a/c binding protein
    • Protein or peptide: FCPII-H1, Fucoxanthin chlorophyll a/c 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: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
  • Ligand: CHLOROPHYLL A
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
KeywordsPSII-FCPII / PHOTOSYNTHESIS
Biological speciesStephanocyclus meneghinianus (Diatom)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsShen LL / Li ZH / Shen JR / Wang WD
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana.
Authors: Songhao Zhao / Lili Shen / Xiaoyi Li / Qiushuang Tao / Zhenhua Li / Caizhe Xu / Cuicui Zhou / Yanyan Yang / Min Sang / Guangye Han / Long-Jiang Yu / Tingyun Kuang / Jian-Ren Shen / Wenda Wang /
Abstract: Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific ...Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific fucoxanthin chlorophyll-binding proteins (FCPs) to enhance the blue-green light absorption under water. We purified a photosystem II (PSII)-FCPII supercomplex and a trimeric FCP from Cyclotella meneghiniana (Cm) and solved their structures by cryo-electron microscopy (cryo-EM). The structures reveal detailed organizations of monomeric, dimeric and trimeric FCP antennae, as well as distinct assemblies of Lhcx6_1 and dimeric FCPII-H in PSII core. Each Cm-PSII-FCPII monomer contains an Lhcx6_1, an FCP heterodimer and other three FCP monomers, which form an efficient pigment network for harvesting energy. More diadinoxanthins and diatoxanthins are found in FCPs, which may function to quench excess energy. The trimeric FCP contains more chlorophylls c and fucoxanthins. These diversified FCPs and PSII-FCPII provide a structural basis for efficient light energy harvesting, transfer, and dissipation in C. meneghiniana.
History
DepositionAug 24, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37267.png

Downloads & links

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Map

FileDownload / File: emd_37267.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.313
Minimum - Maximum-0.44214472 - 0.87280774
Average (Standard dev.)-0.0007294239 (±0.010722723)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 542.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37267_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_37267_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Cm-PSII-FCPII-G/H

EntireName: Cm-PSII-FCPII-G/H
Components
  • Complex: Cm-PSII-FCPII-G/H
    • Protein or peptide: FCPII-G, Fucoxanthin chlorophyll a/c binding protein
    • Protein or peptide: FCPII-H2, Fucoxanthin chlorophyll a/c binding protein
    • Protein or peptide: FCPII-H1, Fucoxanthin chlorophyll a/c 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: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
  • Ligand: CHLOROPHYLL A
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: (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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Supramolecule #1: Cm-PSII-FCPII-G/H

SupramoleculeName: Cm-PSII-FCPII-G/H / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: PSII-FCPII-G/H complex in the PSII-FCPII supercomplex from Cyclotella meneghiniana
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)

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Macromolecule #1: FCPII-G, Fucoxanthin chlorophyll a/c binding protein

MacromoleculeName: FCPII-G, Fucoxanthin chlorophyll a/c binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 18.512004 KDa
SequenceString:
APPGLVGALP PVGFFDPAGF AAKASPEELS RYREVEIMHG RFAQLAVLGF IIPEKCAYDG SFGDDFLAPT GRALEVFNTD PLWLGLTLA VISALETVRL IETEPGTRTD AKIESLGWRP KTESEYINYQ VRELQQGRLA MLAFAGEVAQ ELVNDKPLLV N LQDSGFVS W

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Macromolecule #2: FCPII-H2, Fucoxanthin chlorophyll a/c binding protein

MacromoleculeName: FCPII-H2, Fucoxanthin chlorophyll a/c binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 18.251734 KDa
SequenceString:
FENELGVIAP TGFFDPLGLS KNISKEKFDE YRTAELKHGR AAMLAVLGYI APETYRFGFD IAPGVSTYDI PNGVAAIDYI PALGWAQII FLIGAVDYWG VLGDFSFGKP DLGDKEEERK LQELQHGRLA MLAFLELLRH DSQNFVSPGF DGYDKMITGL P FMYG

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Macromolecule #3: FCPII-H1, Fucoxanthin chlorophyll a/c binding protein

MacromoleculeName: FCPII-H1, Fucoxanthin chlorophyll a/c binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 18.085545 KDa
SequenceString:
FENELGVIAP TGFFDPLGFT QDIDQEKFDQ YRTAELKHGR VAQLAVVGYV VPEFFRWGFD IAPGIACADV PNGVAAINAI PALGWAQII FAIGAVDVRG WFGNFDIGKP DLKGKEEERA LQELQHGRLA MLAILELLRH DSQNLVKPGF DGLDNLITGL P FLYN

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Macromolecule #4: (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: 4 / Number of copies: 6 / Formula: A86
Molecular weightTheoretical: 658.906 Da

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Macromolecule #5: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...

MacromoleculeName: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen- ...Name: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
type: ligand / ID: 5 / Number of copies: 1 / Formula: ET4
Molecular weightTheoretical: 566.856 Da
Chemical component information

ChemComp-ET4:
(1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol

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Macromolecule #6: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 6 / Number of copies: 36 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #7: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 7 / Number of copies: 3 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #8: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 8 / Number of copies: 1 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #9: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 9 / Number of copies: 1 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

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Macromolecule #10: (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: 10 / Number of copies: 4 / 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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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 K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 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: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 314409
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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