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- PDB-9uc6: Cryo-EM structure of the Lhcp trimer from Ostreococcus tauri at 1... -

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Basic information

Entry
Database: PDB / ID: 9uc6
TitleCryo-EM structure of the Lhcp trimer from Ostreococcus tauri at 1.94 angstrom resolution
ComponentsChlorophyll a-b binding protein, chloroplastic
KeywordsPHOTOSYNTHESIS / LHCp / Prasinophytes / green light absorption / carotenoid / Light-harvesting complex / prasinoxanthin / micromonal / dihydrolutein / uriolide / acyl-antheraxanthin / DVP.
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
: / : / : / : / : / Lauryl Maltose Neopentyl Glycol / CHLOROPHYLL B / CHLOROPHYLL A / Chem-IWJ / Chem-NEX ...: / : / : / : / : / Lauryl Maltose Neopentyl Glycol / CHLOROPHYLL B / CHLOROPHYLL A / Chem-IWJ / Chem-NEX / Chem-SQD / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesOstreococcus tauri (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.94 Å
AuthorsSeki, S. / Kubota, M. / Ishii, A. / Kim, E. / Tanaka, H. / Miyata, T. / Namba, K. / Kurisu, G. / Minagawa, J. / Fujii, R.
Funding support Japan, 7items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP23ama121003 Japan
Japan Society for the Promotion of Science (JSPS)K23KJ1834 Japan
Japan Science and TechnologyJPMJFS2138 Japan
Japan Science and TechnologyJPMJCR20E1 Japan
Japan Society for the Promotion of Science (JSPS)23H04958 Japan
Japan Society for the Promotion of Science (JSPS)21H05040 Japan
Japan Society for the Promotion of Science (JSPS)23H04960 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of the LHCp trimer from Ostreococcus tauri at 1.94 angstrom resolution
Authors: Soichiro, S. / Kubota, M. / Ishii, A. / Kim, E. / Tomoko, M. / Hideaki, T. / Keiichi, N. / Genji, K. / Minagawa, J. / Ritsuko, F.
History
DepositionApr 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chlorophyll a-b binding protein, chloroplastic
B: Chlorophyll a-b binding protein, chloroplastic
C: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,43272
Polymers64,2543
Non-polymers55,17869
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 21417.949 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ostreococcus tauri (plant) / References: UniProt: Q3B9V0

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Non-polymers , 12 types, 255 molecules

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


Mass: 893.489 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1L0F / Mg-2,4-divinyl-phaeoporphyrin a5-monometyl ester


Mass: 610.941 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H30MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical ChemComp-A1LYY / (5~{Z})-3-[2-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]ethyl]-5-[(2~{E},4~{E},6~{E},8~{E},10~{E},12~{E})-2,7,11-trimethyl-13-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]trideca-2,4,6,8,10,12-hexaenylidene]furan-2-one / Uriolide


Mass: 614.854 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H54O5 / Feature type: SUBJECT OF INVESTIGATION
#7: 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.: 3 / Source method: obtained synthetically / Formula: C40H56O4
#8: Chemical ChemComp-A1LYX / (2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-6,11,15-trimethyl-17-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]-2-[2-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]ethyl]heptadeca-2,4,6,8,10,12,14,16-octaenal / Micromonal


Mass: 584.871 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H56O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-A1L0E / (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-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15-octaenyl]cyclohex-3-en-1-ol / 7',8'-dihydrolutein


Mass: 570.887 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H58O2 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-AV0 / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside / 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 1005.188 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C47H88O22
#11: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-A1LYW / [(1~{S},3~{S},6~{R})-1,5,5-trimethyl-6-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]-7-oxabicyclo[4.1.0]heptan-3-yl] (~{Z})-oct-2-enoate / 3-octenoyl-8'-s-cis-antheraxanthin B


Mass: 709.051 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C48H68O4 / Feature type: SUBJECT OF INVESTIGATION
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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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: Lhcp trimer from Ostreococcus tauri / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.12 MDa / Experimental value: NO
Source (natural)Organism: Ostreococcus tauri (plant)
Buffer solutionpH: 7.5 / Details: 0.003% LMNG
Buffer componentConc.: 25 mM / Name: HEPES / Formula: C8H18N2O4S
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 3 sec. / Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6144
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2SerialEM4.1.0betaimage acquisition
4cryoSPARC4.2.1CTF correction
7UCSF Chimera1.17.1model fitting
9Coot0.9.4.1model refinement
10PHENIX1.19.2model refinement
11cryoSPARC4.2.1initial Euler assignment
12cryoSPARC4.2.1final Euler assignment
14cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5408616
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 1.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1153594 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8HG3

8hg3


Pdb chain-ID: S / Accession code: 8HG3 / Chain residue range: 32-233 / Pdb chain residue range: 32-233 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 1.94 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.018694
ELECTRON MICROSCOPYf_angle_d1.69312486
ELECTRON MICROSCOPYf_dihedral_angle_d12.4453819
ELECTRON MICROSCOPYf_chiral_restr0.303981
ELECTRON MICROSCOPYf_plane_restr0.0082937

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