7SC8

Synechocystis PCC 6803 Phycobilisome rod from PBS sample


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 1.3 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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin alpha subunit162Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for Q54715 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin beta subunit172Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for Q54714 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome rod-core linker polypeptide CpcGKA [auth BK]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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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1LA [auth BL]291Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for P73203 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2MA [auth BM]273Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rodNA [auth BN]83Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
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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 
AB [auth AI]
AC [auth AZ]
BB [auth AJ]
BC [auth BA]
CB [auth AJ]
AB [auth AI],
AC [auth AZ],
BB [auth AJ],
BC [auth BA],
CB [auth AJ],
CC [auth BB],
DB [auth AK],
DC [auth BB],
EB [auth AL],
EC [auth BC],
FB [auth AL],
FC [auth BD],
GB [auth AM],
GC [auth BD],
HB [auth AN],
HC [auth BE],
IB [auth AN],
IC [auth BF],
JB [auth AO],
JC [auth BF],
KB [auth AP],
KC [auth BG],
LB [auth AP],
LC [auth BH],
MB [auth AQ],
MC [auth BH],
NB [auth AR],
NC [auth BI],
OA [auth AA],
OB [auth AR],
OC [auth BJ],
PA [auth AB],
PB [auth AS],
PC [auth BJ],
QA [auth AB],
QB [auth AT],
RA [auth AC],
RB [auth AT],
SA [auth AD],
SB [auth AU],
TA [auth AD],
TB [auth AV],
UA [auth AE],
UB [auth AV],
VA [auth AF],
VB [auth AW],
WA [auth AF],
WB [auth AX],
XA [auth AG],
XB [auth AX],
YA [auth AH],
YB [auth AY],
ZA [auth AH],
ZB [auth AZ]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.92
RECONSTRUCTIONcryoSPARC3.1

Structure Validation

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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: 2024-11-06
    Changes: Data collection, Structure summary