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- EMDB-25071: Synechocystis PCC 6803 Phycobilisome in the up-up rod conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-25071
TitleSynechocystis PCC 6803 Phycobilisome in the up-up rod conformation
Map dataRefined map of PBS in up-up conformation
Sample
  • Complex: Complex of phycobilisome from Synechocystis PCC 6803 in the up-up conformation
KeywordsComplex / light harvesting / pigment / PHOTOSYNTHESIS
Biological speciesSynechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSauer PV / Sutter M / Dominguez-Martin MA / Kirst H / Kerfeld CA
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN795070European Union
CitationJournal: Nature / Year: 2022
Title: Structures of a phycobilisome in light-harvesting and photoprotected states.
Authors: María Agustina Domínguez-Martín / Paul V Sauer / Henning Kirst / Markus Sutter / David Bína / Basil J Greber / Eva Nogales / Tomáš Polívka / Cheryl A Kerfeld /
Abstract: Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae. These large protein complexes capture incident sunlight and transfer the energy through a network of embedded ...Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae. These large protein complexes capture incident sunlight and transfer the energy through a network of embedded pigment molecules called bilins to the photosynthetic reaction centres. However, light harvesting must also be balanced against the risks of photodamage. A known mode of photoprotection is mediated by orange carotenoid protein (OCP), which binds to PBS when light intensities are high to mediate photoprotective, non-photochemical quenching. Here we use cryogenic electron microscopy to solve four structures of the 6.2 MDa PBS, with and without OCP bound, from the model cyanobacterium Synechocystis sp. PCC 6803. The structures contain a previously undescribed linker protein that binds to the membrane-facing side of PBS. For the unquenched PBS, the structures also reveal three different conformational states of the antenna, two previously unknown. The conformational states result from positional switching of two of the rods and may constitute a new mode of regulation of light harvesting. Only one of the three PBS conformations can bind to OCP, which suggests that not every PBS is equally susceptible to non-photochemical quenching. In the OCP-PBS complex, quenching is achieved through the binding of four 34 kDa OCPs organized as two dimers. The complex reveals the structure of the active form of OCP, in which an approximately 60 Å displacement of its regulatory carboxy terminal domain occurs. Finally, by combining our structure with spectroscopic properties, we elucidate energy transfer pathways within PBS in both the quenched and light-harvesting states. Collectively, our results provide detailed insights into the biophysical underpinnings of the control of cyanobacterial light harvesting. The data also have implications for bioengineering PBS regulation in natural and artificial light-harvesting systems.
History
DepositionSep 30, 2021-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25071.png

Downloads & links

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Map

FileDownload / File: emd_25071.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined map of PBS in up-up conformation
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 720 pix.
= 756. Å		1.05 Å/pix.
x 720 pix.
= 756. Å		1.05 Å/pix.
x 720 pix.
= 756. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.221
Minimum - Maximum-0.9280692 - 2.383903
Average (Standard dev.)-0.0016599895 (±0.0561896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 755.99994 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25071_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Map sharpened with deepEMhancer on tight preset

Fileemd_25071_additional_1.map
AnnotationMap sharpened with deepEMhancer on tight preset
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_25071_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_25071_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Complex of phycobilisome from Synechocystis PCC 6803 in the up-up...

EntireName: Complex of phycobilisome from Synechocystis PCC 6803 in the up-up conformation
Components
  • Complex: Complex of phycobilisome from Synechocystis PCC 6803 in the up-up conformation

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Supramolecule #1: Complex of phycobilisome from Synechocystis PCC 6803 in the up-up...

SupramoleculeName: Complex of phycobilisome from Synechocystis PCC 6803 in the up-up conformation
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)

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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

Concentration3.8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Details: Streptavidin affinity grid, home made
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV / Details: Manual blotting.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsStreptavidin lattice was subtracted after movie alignment.
Startup modelType of model: OTHER / Details: Ab initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 135701
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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