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- EMDB-41463: Synechocystis PCC 6803 Phycobilisome quenched by OCP, high resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-41463
TitleSynechocystis PCC 6803 Phycobilisome quenched by OCP, high resolution
Map data
Sample
  • Complex: Phycobilisome in complex with OCP
KeywordsComplex / light harvesting / pigment / PHOTOSYNTHESIS
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsSauer PV / Sutter M / Cupellini L
Funding support United States, European Union, Czech Republic, 4 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020606 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127018 United States
European Research Council (ERC)786714European Union
Czech Science Foundation19-28323X Czech Republic
CitationJournal: Sci Adv / Year: 2024
Title: Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes.
Authors: Paul V Sauer / Lorenzo Cupellini / Markus Sutter / Mattia Bondanza / María Agustina Domínguez Martin / Henning Kirst / David Bína / Adrian Fujiet Koh / Abhay Kotecha / Basil J Greber / ...Authors: Paul V Sauer / Lorenzo Cupellini / Markus Sutter / Mattia Bondanza / María Agustina Domínguez Martin / Henning Kirst / David Bína / Adrian Fujiet Koh / Abhay Kotecha / Basil J Greber / Eva Nogales / Tomáš Polívka / Benedetta Mennucci / Cheryl A Kerfeld /
Abstract: Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) ...Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria.
History
DepositionAug 4, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41463.png

Downloads & links

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Map

FileDownload / File: emd_41463.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 768 pix.
= 744.192 Å		0.97 Å/pix.
x 768 pix.
= 744.192 Å		0.97 Å/pix.
x 768 pix.
= 744.192 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.969 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.67200774 - 2.2069356
Average (Standard dev.)-0.0015121007 (±0.049966585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 744.192 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41463_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_41463_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_41463_half_map_2.map
Projections & Slices
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Sample components

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Entire : Phycobilisome in complex with OCP

EntireName: Phycobilisome in complex with OCP
Components
  • Complex: Phycobilisome in complex with OCP

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Supramolecule #1: Phycobilisome in complex with OCP

SupramoleculeName: Phycobilisome in complex with OCP / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Synechocystis sp. PCC 6803 (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: 7.4
GridModel: Quantifoil / Support film - Material: GOLD / Support film - topology: HOLEY
Details: Grids were coated with streptavidin crystal in-house
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

25068

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 153576
FSC plot (resolution estimation)

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