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- EMDB-34733: Cryo-EM structure of the Lhcp complex from Ostreococcus tauri -

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Basic information

Entry
Database: EMDB / ID: EMD-34733
TitleCryo-EM structure of the Lhcp complex from Ostreococcus tauri
Map data
Sample
  • Complex: Prasinophyte-specific Lhc protein (Lhcp) complex
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL A
  • Ligand: CHLOROPHYLL B
  • Ligand: Chlorophyll c2
  • Ligand: (1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol
  • 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: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one
Function / homologyphotosynthesis, light harvesting / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / Chlorophyll a-b binding protein, chloroplastic
Function and homology information
Biological speciesOstreococcus tauri (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsShan J / Sheng X / Ishii A / Watanabe A / Song C / Murata K / Minagawa J / Liu Z
Funding support Japan, China, 4 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H04778 and 21H05040 Japan
Chinese Academy of SciencesXDB37020101 and YSBR-015 China
National Natural Science Foundation of China (NSFC)31925024 China
Ministry of Science and Technology (MoST, China)2017YFA0503702 China
CitationJournal: Elife / Year: 2023
Title: The photosystem I supercomplex from a primordial green alga harbors three light-harvesting complex trimers.
Authors: Asako Ishii / Jianyu Shan / Xin Sheng / Eunchul Kim / Akimasa Watanabe / Makio Yokono / Chiyo Noda / Chihong Song / Kazuyoshi Murata / Zhenfeng Liu / Jun Minagawa /
Abstract: As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in ...As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in photosynthesis. Here, we report the structure and function of the photosystem I (PSI) supercomplex in low light conditions, where it expands its photon-absorbing capacity by assembling with the light-harvesting complexes I (LHCI) and a prasinophyte-specific light-harvesting complex (Lhcp). The architecture of the supercomplex exhibits hybrid features of the plant-type and the green algal-type PSI supercomplexes, consisting of a PSI core, an Lhca1-Lhca4-Lhca2-Lhca3 belt attached on one side and an Lhca5-Lhca6 heterodimer associated on the other side between PsaG and PsaH. Interestingly, nine Lhcp subunits, including one Lhcp1 monomer with a phosphorylated amino-terminal threonine and eight Lhcp2 monomers, oligomerize into three trimers and associate with PSI on the third side between Lhca6 and PsaK. The Lhcp1 phosphorylation and the light-harvesting capacity of PSI were subjected to reversible photoacclimation, suggesting that the formation of PSI-LHCI-Lhcp supercomplex is likely due to a phosphorylation-dependent mechanism induced by changes in light intensity. Notably, this supercomplex did not exhibit far-red peaks in the 77 K fluorescence spectra, which is possibly due to the weak coupling of the chlorophyll 603-609 pair in Lhca1-4.
History
DepositionNov 13, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateApr 26, 2023-
Current statusApr 26, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34733.png

Downloads & links

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Map

FileDownload / File: emd_34733.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.049495555 - 0.08097579
Average (Standard dev.)2.8518354e-05 (±0.0021259575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 399.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34733_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_34733_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 : Prasinophyte-specific Lhc protein (Lhcp) complex

EntireName: Prasinophyte-specific Lhc protein (Lhcp) complex
Components
  • Complex: Prasinophyte-specific Lhc protein (Lhcp) complex
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL A
  • Ligand: CHLOROPHYLL B
  • Ligand: Chlorophyll c2
  • Ligand: (1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol
  • 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: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one

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Supramolecule #1: Prasinophyte-specific Lhc protein (Lhcp) complex

SupramoleculeName: Prasinophyte-specific Lhc protein (Lhcp) complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Ostreococcus tauri (plant) / Strain: OTH95 / Organelle: chloroplast / Location in cell: thylakoid membrane

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Macromolecule #1: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ostreococcus tauri (plant)
Molecular weightTheoretical: 24.689807 KDa
Recombinant expressionOrganism: Ostreococcus tauri (plant)
SequenceString: MSALLASSFV SRVAAFKAQK VQNKSVSTTV KADIYPEFGT YPGGGESPII PFGSEKNAER EVIHGRWAML GVTGAWAAEN GTGIPWFTA GTLCTPDDCT AVADKFPGAV APLAPEGSGY PSFWNVLIIE IVLVGAAEAY RTGISDSPFD DGLTVGDVNP G GRFDPLGL ...String:
MSALLASSFV SRVAAFKAQK VQNKSVSTTV KADIYPEFGT YPGGGESPII PFGSEKNAER EVIHGRWAML GVTGAWAAEN GTGIPWFTA GTLCTPDDCT AVADKFPGAV APLAPEGSGY PSFWNVLIIE IVLVGAAEAY RTGISDSPFD DGLTVGDVNP G GRFDPLGL AESGDLEELK IKELKHCRLS MFAWLGCIFQ ALATQEGPIA NWQSHVADPV HSNVLTNAAK GFGFY

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Macromolecule #2: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 2 / Number of copies: 24 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #3: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 3 / Number of copies: 15 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #4: Chlorophyll c2

MacromoleculeName: Chlorophyll c2 / type: ligand / ID: 4 / Number of copies: 3 / Formula: KC2
Molecular weightTheoretical: 608.926 Da
Chemical component information

ChemComp-KC2:
Chlorophyll c2 / Chlorophyll c

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Macromolecule #5: (1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...

MacromoleculeName: (1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca- ...Name: (1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol
type: ligand / ID: 5 / Number of copies: 12 / Formula: Q6L
Molecular weightTheoretical: 570.887 Da
Chemical component information

ChemComp-Q6L:
(1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol

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Macromolecule #6: (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: 6 / Number of copies: 2 / 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 #7: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4...

MacromoleculeName: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl- ...Name: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one
type: ligand / ID: 7 / Number of copies: 6 / Formula: IWJ
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-IWJ:
(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one

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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
Component:
ConcentrationFormulaName
25.0 mMMES2-(N-morpholino)ethanesulfonic acid
1.0 %A8-35Amiphipol 8-35

Details: 25mM MES-NaOH,pH 6.5 1% A8-35
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER / Details: none
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV / Details: Vitrification carried out in air atmosphere.
DetailsThis sample is

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5288217
Startup modelType of model: EMDB MAP
EMDB ID:

30536

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 10 / Avg.num./class: 30000 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 4 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 80573
DetailsThe selected images were aligned by the beam-induced motion
FSC plot (resolution estimation)

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