8TO5

Central rod disk in C1 symmetry of high-resolution phycobilisome quenched by OCP (local refinement)

  • Classification: PHOTOSYNTHESIS
  • Organism(s): Synechocystis sp. PCC 6803
  • Mutation(s): No 

  • Deposited: 2023-08-02 Released: 2024-04-17 
  • Deposition Author(s): Sauer, P.V., Sutter, M., Cupellini, L.
  • Funding Organization(s): European Research Council (ERC), Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Czech Science Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes.

Sauer, P.V.Cupellini, L.Sutter, M.Bondanza, M.Dominguez Martin, M.A.Kirst, H.Bina, D.Koh, A.F.Kotecha, A.Greber, B.J.Nogales, E.Polivka, T.Mennucci, B.Kerfeld, C.A.

(2024) Sci Adv 10: eadk7535-eadk7535

  • DOI: https://doi.org/10.1126/sciadv.adk7535
  • Primary Citation of Related Structures:  
    8TO2, 8TO5, 8TPJ, 8TRO

  • PubMed 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) 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.


  • Organizational Affiliation

    California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin alpha subunit162Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
Find proteins for Q54715 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore Q54715 
Go to UniProtKB:  Q54715
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54715
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin beta subunit172Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
Find proteins for Q54714 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore Q54714 
Go to UniProtKB:  Q54714
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54714
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1M [auth b]291Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
Find proteins for P73203 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P73203 
Go to UniProtKB:  P73203
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UniProt GroupP73203
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2N [auth c]273Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
Find proteins for P73204 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P73204 
Go to UniProtKB:  P73204
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UniProt GroupP73204
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
AA [auth U]
BA [auth V]
CA [auth V]
DA [auth W]
EA [auth X]
AA [auth U],
BA [auth V],
CA [auth V],
DA [auth W],
EA [auth X],
FA [auth X],
O [auth M],
P [auth N],
Q [auth N],
R [auth O],
S [auth P],
T [auth P],
U [auth Q],
V [auth R],
W [auth R],
X [auth S],
Y [auth T],
Z [auth T]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B [auth N]
D [auth P]
F [auth R]
H [auth T]
J [auth V]
B [auth N],
D [auth P],
F [auth R],
H [auth T],
J [auth V],
L [auth X]
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionGrant ERC-AdG 786714 (LIFETimeS)
Department of Energy (DOE, United States)United StatesDE-SC0020606
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127018
Czech Science FoundationCzech Republic19-28323X

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release