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- EMDB-34883: Bry-LHCII homotrimer of Bryopsis corticulans -

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Basic information

Entry
Database: EMDB / ID: EMD-34883
TitleBry-LHCII homotrimer of Bryopsis corticulans
Map data
Sample
  • Complex: Bryopsis corticulans chlorophyll a/b-type light-harvesting complex II homotrimer
    • Protein or peptide: Siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
  • Ligand: Siphonein
  • Ligand: Siphonaxanthin
  • Ligand: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
Keywordslight-harvesting complexes / siphonaxanthin / siphonein / PHOTOSYNTHESIS
Biological speciesBryopsis corticulans (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsLi ZH / Shen JR / Wang WD
Funding support China, 9 items
OrganizationGrant numberCountry
Chinese Academy of Sciences2019YFA0906300 China
Chinese Academy of Sciences2021YFA1300403 China
Chinese Academy of SciencesXDA26050402 China
Chinese Academy of SciencesXDB17000000 China
Chinese Academy of Sciences2020081 China
Chinese Academy of SciencesJCTD-2020-06 China
Chinese Academy of SciencesYSBR-004 China
Chinese Academy of Sciences31970260 China
Chinese Academy of Sciences32222007 China
CitationJournal: Structure / Year: 2023
Title: Structural and functional properties of different types of siphonous LHCII trimers from an intertidal green alga Bryopsis corticulans.
Authors: Zhenhua Li / Cuicui Zhou / Songhao Zhao / Jinyang Zhang / Xueyang Liu / Min Sang / Xiaochun Qin / Yanyan Yang / Guangye Han / Tingyun Kuang / Jian-Ren Shen / Wenda Wang /
Abstract: Light-harvesting complexes of photosystem II (LHCIIs) in green algae and plants are vital antenna apparatus for light harvesting, energy transfer, and photoprotection. Here we determined the ...Light-harvesting complexes of photosystem II (LHCIIs) in green algae and plants are vital antenna apparatus for light harvesting, energy transfer, and photoprotection. Here we determined the structure of a siphonous-type LHCII trimer from the intertidal green alga Bryopsis corticulans by X-ray crystallography and cryo-electron microscopy (cryo-EM), and analyzed its functional properties by spectral analysis. The Bryopsis LHCII (Bry-LHCII) structures in both homotrimeric and heterotrimeric form show that green light-absorbing siphonaxanthin and siphonein occupied the sites of lutein and violaxanthin in plant LHCII, and two extra chlorophylls (Chls) b replaced Chls a. Binding of these pigments expands the blue-green light absorption of B. corticulans in the tidal zone. We observed differences between the Bry-LHCII homotrimer crystal and cryo-EM structures, and also between Bry-LHCII homotrimer and heterotrimer cryo-EM structures. These conformational changes may reflect the flexibility of Bry-LHCII, which may be required to adapt to light fluctuations from tidal rhythms.
History
DepositionDec 1, 2022-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34883.png

Downloads & links

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Map

FileDownload / File: emd_34883.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 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: 0.207
Minimum - Maximum-0.28215462 - 0.9033468
Average (Standard dev.)0.0021250849 (±0.023695972)
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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Half map: #2

Fileemd_34883_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_34883_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 : Bryopsis corticulans chlorophyll a/b-type light-harvesting comple...

EntireName: Bryopsis corticulans chlorophyll a/b-type light-harvesting complex II homotrimer
Components
  • Complex: Bryopsis corticulans chlorophyll a/b-type light-harvesting complex II homotrimer
    • Protein or peptide: Siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
  • Ligand: Siphonein
  • Ligand: Siphonaxanthin
  • Ligand: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

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Supramolecule #1: Bryopsis corticulans chlorophyll a/b-type light-harvesting comple...

SupramoleculeName: Bryopsis corticulans chlorophyll a/b-type light-harvesting complex II homotrimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bryopsis corticulans (plant)

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Macromolecule #1: Siphonaxanthin chlorophyll a/b binding light-harvesting complex I...

MacromoleculeName: Siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 26.696133 KDa
SequenceString: MASAMIAQTV VGAQAARATK QVTRAAVEFY GPDRALWLGP YSEGAVPSYL TGEFPGDYGW DSAGLSADPE TFAANRELEL IHARWAMLG TVGCLTPEAL EKYGGVEFGE AVWFKAGSQI FAEGGLDYLG NPSLVHAQSI LAICWTQVVL MGLAEGYRCS G GPLGEATD ...String:
MASAMIAQTV VGAQAARATK QVTRAAVEFY GPDRALWLGP YSEGAVPSYL TGEFPGDYGW DSAGLSADPE TFAANRELEL IHARWAMLG TVGCLTPEAL EKYGGVEFGE AVWFKAGSQI FAEGGLDYLG NPSLVHAQSI LAICWTQVVL MGLAEGYRCS G GPLGEATD PLYPGEAFDP MGMADDPETF AELKTKEIKN GRLAMFAMFG FFVQSLQTGK GPVECWAEHI ADPVANNGFV YA TKFFGAQ IF

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Macromolecule #2: Siphonein

MacromoleculeName: Siphonein / type: ligand / ID: 2 / Number of copies: 3 / Formula: 0UR
Molecular weightTheoretical: 781.157 Da
Chemical component information

ChemComp-0UR:
Siphonein

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Macromolecule #3: Siphonaxanthin

MacromoleculeName: Siphonaxanthin / type: ligand / ID: 3 / Number of copies: 6 / Formula: 0IE
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-0IE:
Siphonaxanthin

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Macromolecule #4: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
type: ligand / ID: 4 / Number of copies: 3 / Formula: NEX
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-NEX:
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL

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Macromolecule #5: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 5 / Number of copies: 24 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #6: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 6 / Number of copies: 18 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
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: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 614955
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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