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- PDB-8hw1: Far-red light-harvesting complex of Antarctic alga Prasiola crispa -

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Basic information

Entry
Database: PDB / ID: 8hw1
TitleFar-red light-harvesting complex of Antarctic alga Prasiola crispa
ComponentsFar-red light-harvesting complex
KeywordsPHOTOSYNTHESIS / undecameric ring / light-harvesting complex
Function / homologyChem-32N / CHLOROPHYLL A / Chem-XAT
Function and homology information
Biological speciesPrasiola crispa (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsKosugi, M. / Kawasaki, M. / Shibata, Y. / Moriya, T. / Adachi, N. / Senda, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17K19431 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H03187 Japan
Japan Agency for Medical Research and Development (AMED)JP20am0101071 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Uphill energy transfer mechanism for photosynthesis in an Antarctic alga.
Authors: Makiko Kosugi / Masato Kawasaki / Yutaka Shibata / Kojiro Hara / Shinichi Takaichi / Toshio Moriya / Naruhiko Adachi / Yasuhiro Kamei / Yasuhiro Kashino / Sakae Kudoh / Hiroyuki Koike / Toshiya Senda /
Abstract: Prasiola crispa, an aerial green alga, forms layered colonies under the severe terrestrial conditions of Antarctica. Since only far-red light is available at a deep layer of the colony, P. crispa has ...Prasiola crispa, an aerial green alga, forms layered colonies under the severe terrestrial conditions of Antarctica. Since only far-red light is available at a deep layer of the colony, P. crispa has evolved a molecular system for photosystem II (PSII) excitation using far-red light with uphill energy transfer. However, the molecular basis underlying this system remains elusive. Here, we purified a light-harvesting chlorophyll (Chl)-binding protein complex from P. crispa (Pc-frLHC) that excites PSII with far-red light and revealed its ring-shaped structure with undecameric 11-fold symmetry at 3.13 Å resolution. The primary structure suggests that Pc-frLHC evolved from LHCI rather than LHCII. The circular arrangement of the Pc-frLHC subunits is unique among eukaryote LHCs and forms unprecedented Chl pentamers at every subunit‒subunit interface near the excitation energy exit sites. The Chl pentamers probably contribute to far-red light absorption. Pc-frLHC's unique Chl arrangement likely promotes PSII excitation with entropy-driven uphill excitation energy transfer.
History
DepositionDec 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Far-red light-harvesting complex
B: Far-red light-harvesting complex
C: Far-red light-harvesting complex
D: Far-red light-harvesting complex
E: Far-red light-harvesting complex
F: Far-red light-harvesting complex
G: Far-red light-harvesting complex
H: Far-red light-harvesting complex
I: Far-red light-harvesting complex
J: Far-red light-harvesting complex
K: Far-red light-harvesting complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)489,606154
Polymers368,45111
Non-polymers121,155143
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Far-red light-harvesting complex


Mass: 33495.516 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Prasiola crispa (plant)
#2: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 121 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-32N / (1S)-4-[(1E,3Z,5E,7E,9E,11E,13E,15E,17E)-3-(hydroxymethyl)-7,12,16-trimethyl-18-[(1R,4S)-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]-3,5,5-trimethyl-cyclohex-3-en-1-ol


Mass: 584.871 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C40H56O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: Far-red light-harvesting complex / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.7 MDa / Experimental value: YES
Source (natural)Organism: Prasiola crispa (plant)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameBuffer-ID
125 mMMES1
20.015 %beta-DDM1
30.5 Mbetain1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid 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: 291 K / Details: blot time 5 sec blot force 25

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 92000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 64.92 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1555

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4GctfCTF correction
7PHENIX1.18model fitting
8Coot0.8.9.2model fitting
10PHENIX1.18model refinement
11Coot0.8.9.2model refinement
12RELION3.1initial Euler assignment
13RELION3.1final Euler assignment
14RELION3.1classification
15RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 696095
SymmetryPoint symmetry: C11 (11 fold cyclic)
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99510 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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