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Open data
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Basic information
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Title | Cryo-EM structure of the prasinophyte-specific light-harvesting complex (Lhcp)from Ostreococcus tauri | |||||||||||||||
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![]() | Complex / Electron transport / Light-harvesting / Photosynthesis | |||||||||||||||
Function / homology | ![]() photosynthesis, light harvesting in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.44 Å | |||||||||||||||
![]() | Shan J / Sheng X / Ishii A / Watanabe A / Song C / Murata K / Minagawa J / Liu Z | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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. | |||||||||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 157.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.4 KB 17.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.3 KB | Display | ![]() |
Images | ![]() | 52.5 KB | ||
Others | ![]() ![]() | 172 MB 172 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hg6MC ![]() 7ycaC ![]() 8hg3C ![]() 8hg5C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34736_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34736_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Prasinophyte-specific Lhc protein (Lhcp) complex
Entire | Name: Prasinophyte-specific Lhc protein (Lhcp) complex |
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Components |
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-Supramolecule #1: Prasinophyte-specific Lhc protein (Lhcp) complex
Supramolecule | Name: Prasinophyte-specific Lhc protein (Lhcp) complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Chlorophyll a-b binding protein, chloroplastic
Macromolecule | Name: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.689807 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #2: CHLOROPHYLL A
Macromolecule | Name: CHLOROPHYLL A / type: ligand / ID: 2 / Number of copies: 24 / Formula: CLA |
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Molecular weight | Theoretical: 893.489 Da |
Chemical component information | ![]() ChemComp-CLA: |
-Macromolecule #3: CHLOROPHYLL B
Macromolecule | Name: CHLOROPHYLL B / type: ligand / ID: 3 / Number of copies: 15 / Formula: CHL |
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Molecular weight | Theoretical: 907.472 Da |
Chemical component information | ![]() ChemComp-CHL: |
-Macromolecule #4: Chlorophyll c2
Macromolecule | Name: Chlorophyll c2 / type: ligand / ID: 4 / Number of copies: 3 / Formula: KC2 |
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Molecular weight | Theoretical: 608.926 Da |
Chemical component information | ![]() ChemComp-KC2: |
-Macromolecule #5: (1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...
Macromolecule | 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- ...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 |
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Molecular weight | Theoretical: 570.887 Da |
Chemical component information | ![]() ChemComp-Q6L: |
-Macromolecule #6: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4...
Macromolecule | 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- ...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: 6 / Number of copies: 5 / Formula: IWJ |
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Molecular weight | Theoretical: 600.87 Da |
Chemical component information | ![]() ChemComp-IWJ: |
-Macromolecule #7: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...
Macromolecule | Name: (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: 7 / Number of copies: 1 / Formula: NEX |
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Molecular weight | Theoretical: 600.87 Da |
Chemical component information | ![]() ChemComp-NEX: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 6.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-8hg6: |