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- EMDB-35080: Far-red light-harvesting complex of Antarctic alga Prasiola crispa -

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Basic information

Entry
Database: EMDB / ID: EMD-35080
TitleFar-red light-harvesting complex of Antarctic alga Prasiola crispa
Map data
Sample
  • Complex: Far-red light-harvesting complex
Biological speciesPrasiola crispa (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsKosugi M / Kawasaki M / Shibata Y / Moriya T / Adachi N / Senda T
Funding support Japan, 3 items
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
DepositionJan 5, 2023-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35080.png

Downloads & links

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Map

FileDownload / File: emd_35080.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 250 pix.
= 282.5 Å		1.13 Å/pix.
x 250 pix.
= 282.5 Å		1.13 Å/pix.
x 250 pix.
= 282.5 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.22933911 - 0.41461942
Average (Standard dev.)1.1167961e-05 (±0.015445859)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 282.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_35080_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35080_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Far-red light-harvesting complex

EntireName: Far-red light-harvesting complex
Components
  • Complex: Far-red light-harvesting complex

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Supramolecule #1: Far-red light-harvesting complex

SupramoleculeName: Far-red light-harvesting complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Prasiola crispa (plant)
Molecular weightTheoretical: 700 KDa

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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

Concentration6 mg/mL
BufferpH: 6.5
Component:
ConcentrationName
25.0 mMMES
0.015 %beta-DDM
0.5 Mbetain
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 5 sec blot force 25.

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1555 / Average exposure time: 64.92 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 92000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 696095
Startup modelType of model: OTHER
Details: An ab initio model was generated using RELION3's own implementation of Stochastic Gradient Descent (SGD) algorithm and low-pass filtered to 60 A for use as an initial model for 3D classification.
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 99510
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 2 / Avg.num./class: 80078 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

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

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