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- PDB-8hg3: Cryo-EM structure of the Lhcp complex from Ostreococcus tauri -

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Basic information

Entry
Database: PDB / ID: 8hg3
TitleCryo-EM structure of the Lhcp complex from Ostreococcus tauri
ComponentsChlorophyll a-b binding protein, chloroplastic
KeywordsELECTRON TRANSPORT / Complex / Light-harvesting / Photosynthesis
Function / homology
Function and homology information


photosynthesis, light harvesting / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid 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
CHLOROPHYLL B / CHLOROPHYLL A / Chem-IWJ / Chlorophyll c2 / Chem-NEX / Chem-Q6L / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesOstreococcus tauri (plant)
MethodELECTRON MICROSCOPY / single 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, 4items
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, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: Chlorophyll a-b binding protein, chloroplastic
T: Chlorophyll a-b binding protein, chloroplastic
U: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,61065
Polymers74,0693
Non-polymers48,54062
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 3 molecules STU

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


Mass: 24689.807 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostreococcus tauri (plant) / Gene: OT_ostta16g00450 / Production host: Ostreococcus tauri (plant) / References: UniProt: Q3B9U7

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Non-polymers , 6 types, 62 molecules

#2: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#3: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#4: Chemical ChemComp-KC2 / Chlorophyll c2


Mass: 608.926 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H28MgN4O5
#5: Chemical
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


Mass: 570.887 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C40H58O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical 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 / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL / 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O4
#7: Chemical
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 / Prasinoxanthin


Mass: 600.870 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Prasinophyte-specific Lhc protein (Lhcp) complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Ostreococcus tauri (plant) / Strain: OTH95 / Cellular location: thylakoid membrane / Organelle: chloroplast
Source (recombinant)Organism: Ostreococcus tauri (plant)
Buffer solutionpH: 6.5 / Details: 25mM MES-NaOH,pH 6.5 1% A8-35
Buffer component
IDConc.NameFormulaBuffer-ID
125 mM2-(N-morpholino)ethanesulfonic acidMES1
21 %Amiphipol 8-35A8-351
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample is
Specimen supportDetails: none / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K / Details: Vitrification carried out in air atmosphere

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARC3.1.0particle selection
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
Image processingDetails: The selected images were aligned by the beam-induced motion
CTF correctionType: NONE
Particle selectionNum. of particles selected: 5288217
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80573 / Algorithm: BACK PROJECTION / Num. of class averages: 4 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.017954
ELECTRON MICROSCOPYf_angle_d1.57511574
ELECTRON MICROSCOPYf_dihedral_angle_d18.0651424
ELECTRON MICROSCOPYf_chiral_restr0.075897
ELECTRON MICROSCOPYf_plane_restr0.0111512

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