7SCC | pdb_00007scc

T-cylinder of Synechocystis PCC 6803 Phycobilisome, complex with OCP - local refinement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structures of a phycobilisome in light-harvesting and photoprotected states.

Dominguez-Martin, M.A.Sauer, P.V.Kirst, H.Sutter, M.Bina, D.Greber, B.J.Nogales, E.Polivka, T.Kerfeld, C.A.

(2022) Nature 609: 835-845

  • DOI: https://doi.org/10.1038/s41586-022-05156-4
  • Primary Citation Related Structures: 
    7SC7, 7SC8, 7SC9, 7SCA, 7SCB, 7SCC

  • PubMed Abstract: 

    Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae 1,2 . 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 3-6 . 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 7 , 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.


  • Organizational Affiliation
    • MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.

Macromolecule Content 

  • Total Structure Weight: 902.15 kDa 
  • Atom Count: 42,904 
  • Modeled Residue Count: 5,474 
  • Deposited Residue Count: 8,054 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Allophycocyanin alpha chain161Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for Q01951 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Go to UniProtKB:  Q01951
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UniProt GroupQ01951
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Allophycocyanin beta chain161Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for Q01952 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, coreEA [auth BK],
M [auth AO]
67Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for Q01950 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Phycobiliprotein ApcEFA [auth BM],
N [auth AQ]
896Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 4
UniProt
Find proteins for Q55544 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Orange carotenoid-binding proteinGA [auth BO],
HA [auth BP],
O [auth AS],
P [auth AT]
317Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: slr1963
UniProt
Find proteins for P74102 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Phycobilisome rod-core linker polypeptide CpcGIA [auth BQ],
JA [auth BR],
Q [auth AU],
R [auth AV]
249Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for P73093 (Synechocystis sp. (strain ATCC 27184 / 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
AB [auth AZ]
BB [auth BA]
CB [auth BB]
DB [auth BD]
EB [auth BE]
AB [auth AZ],
BB [auth BA],
CB [auth BB],
DB [auth BD],
EB [auth BE],
FB [auth BF],
GB [auth BG],
HB [auth BH],
IB [auth BI],
KA [auth AA],
LA [auth AB],
MA [auth AC],
NA [auth AD],
OA [auth AE],
PA [auth AF],
QA [auth AH],
RA [auth AI],
SA [auth AJ],
TA [auth AK],
UA [auth AL],
VA [auth AM],
XA [auth AW],
YA [auth AX],
ZA [auth AY]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
45D
(Subject of Investigation/LOI)

Query on 45D



Download:Ideal Coordinates CCD File
JB [auth BP],
WA [auth AS]
beta,beta-carotene-4,4'-dione
C40 H52 O2
FDSDTBUPSURDBL-DKLMTRRASA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.92
RECONSTRUCTIONcryoSPARC3.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Marie Sklodowska-Curie Actions, FragNET ITNEuropean Union795070

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 1.1: 2022-09-14
    Changes: Database references
  • Version 1.2: 2022-10-05
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary