7SC7

Synechocystis PCC 6803 Phycobilisome core from up-down rod conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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 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
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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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin beta chain161Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin subunit alpha-BE [auth AE],
GA [auth BL]
161Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for P72870 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Allophycocyanin subunit beta-18J [auth AK],
LA [auth BR]
169Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for P74551 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core67Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for Q01950 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobiliprotein ApcEBB [auth CL],
Z [auth BD]
896Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
EC: 4
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome rod-core linker polypeptide CpcG249Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Sll1873 proteinBA [auth BG],
DB [auth CO]
121Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
UniProt
Find proteins for P74135 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
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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 
AD [auth AX]
AE [auth CG]
AF [auth DR]
BD [auth AY]
BE [auth CI]
AD [auth AX],
AE [auth CG],
AF [auth DR],
BD [auth AY],
BE [auth CI],
BF [auth DS],
CD [auth AZ],
CE [auth CL],
DD [auth BA],
DE [auth CL],
ED [auth BD],
EE [auth CP],
FD [auth BD],
FE [auth CQ],
GD [auth BH],
GE [auth CR],
HD [auth BI],
HE [auth CS],
IC [auth AA],
ID [auth BJ],
IE [auth CT],
JC [auth AB],
JD [auth BK],
JE [auth CU],
KC [auth AC],
KD [auth BL],
KE [auth CW],
LC [auth AD],
LD [auth BO],
LE [auth CX],
MC [auth AE],
MD [auth BP],
ME [auth CY],
NC [auth AH],
ND [auth BQ],
NE [auth CZ],
OC [auth AI],
OD [auth BR],
OE [auth DA],
PC [auth AJ],
PD [auth BS],
PE [auth DB],
QC [auth AK],
QD [auth BU],
QE [auth DG],
RC [auth AL],
RD [auth BV],
RE [auth DH],
SC [auth AN],
SD [auth BW],
SE [auth DI],
TC [auth AO],
TD [auth BX],
TE [auth DJ],
UC [auth AP],
UD [auth BY],
UE [auth DK],
VC [auth AQ],
VD [auth CB],
VE [auth DL],
WC [auth AR],
WD [auth CC],
WE [auth DN],
XC [auth AU],
XD [auth CD],
XE [auth DO],
YC [auth AV],
YD [auth CE],
YE [auth DP],
ZC [auth AW],
ZD [auth CF],
ZE [auth DQ]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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: 2024-10-09
    Changes: Data collection, Structure summary