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- EMDB-41436: Central rod disk in D3 symmetry of high-resolution phycobilisome ... -

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Basic information

Entry
Database: EMDB / ID: EMD-41436
TitleCentral rod disk in D3 symmetry of high-resolution phycobilisome quenched by OCP (local refinement)
Map datasharpened map
Sample
  • Complex: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: C-phycocyanin beta subunit
KeywordsComplex / light harvesting / pigment / PHOTOSYNTHESIS
Biological speciesSynechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) / Synechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.63 Å
AuthorsSauer PV / Sutter M / Cupellini L / Kirst H / Kerfeld CA
Funding supportEuropean Union, United States, Czech Republic, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)Grant ERC-AdG 786714 (LIFETimeS)European Union
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
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 2, 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_41436.png

Downloads & links

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Map

FileDownload / File: emd_41436.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 372.224 Å		0.73 Å/pix.
x 512 pix.
= 372.224 Å		0.73 Å/pix.
x 512 pix.
= 372.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-2.8303788 - 8.730953
Average (Standard dev.)-0.0014954373 (±0.13222462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 372.224 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41436_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: refined map

Fileemd_41436_additional_1.map
Annotationrefined map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41436_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41436_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP

EntireName: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP
Components
  • Complex: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: C-phycocyanin beta subunit

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Supramolecule #1: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP

SupramoleculeName: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)

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Macromolecule #1: C-phycocyanin alpha subunit

MacromoleculeName: C-phycocyanin alpha subunit / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString:
MKTPLTEAVS TADSQGRFLS STELQIAFGR LRQANAGLQA AKALTDNAQS LVNGAAQAVY NKFPYTTQTQ GNNFAADQRG KDKCARDIGY YLRIVTYCLV AGGTGPLDEY LIAGIDEINR TFDLSPSWYV EALKYIKANH GLSGDARDEA NSYLDYAINA LS

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Macromolecule #2: C-phycocyanin beta subunit

MacromoleculeName: C-phycocyanin beta subunit / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString:
MFDVFTRVVS QADARGEYLS GSQLDALSAT VAEGNKRIDS VNRITGNASA IVSNAARALF AEQPQLIQPG GNAYTSRRMA ACLRDMEIIL RYVTYATFTG DASVLEDRCL NGLRETYVAL GVPGASVAAG VQKMKEAALD IVNDPNGITR GDCSAIVAEI AGYFDRAAAA VA

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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
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: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm
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: EMDB MAP
EMDB ID:

25068

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 435854
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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