8TPJ

Top cylinder bound to OCP from high-resolution phycobilisome quenched by OCP (local refinement)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobiliprotein ApcE896Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
Find proteins for Q55544 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Go to UniProtKB:  Q55544
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UniProt GroupQ55544
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Orange carotenoid-binding proteinB,
C [auth b]
317Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: slr1963
UniProt
Find proteins for P74102 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Go to UniProtKB:  P74102
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UniProt GroupP74102
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, coreD [auth C]67Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
Find proteins for Q02925 (Synechocystis sp. (strain PCC 6714))
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UniProt GroupQ02925
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin alpha chain161Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
Find proteins for Q01951 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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UniProt GroupQ01951
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin beta chain161Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
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UniProt GroupQ01952
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome rod-core linker polypeptide CpcGQ [auth P],
R [auth Q],
S [auth R],
T [auth S]
249Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
Find proteins for P73093 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
AA [auth I]
BA [auth J]
CA [auth K]
DA [auth L]
EA [auth M]
AA [auth I],
BA [auth J],
CA [auth K],
DA [auth L],
EA [auth M],
FA [auth N],
GA [auth O],
V [auth D],
W [auth E],
X [auth F],
Y [auth G],
Z [auth H]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
45D (Subject of Investigation/LOI)
Query on 45D

Download Ideal Coordinates CCD File 
U [auth B]beta,beta-carotene-4,4'-dione
C40 H52 O2
FDSDTBUPSURDBL-DKLMTRRASA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
F [auth E]
H [auth G]
J [auth I]
L [auth K]
N [auth M]
F [auth E],
H [auth G],
J [auth I],
L [auth K],
N [auth M],
P [auth O]
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0020606
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127018
European Research Council (ERC)European Union786714
Czech Science FoundationCzech Republic19-28323X

Revision History  (Full details and data files)

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