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- PDB-7sc7: Synechocystis PCC 6803 Phycobilisome core from up-down rod confor... -

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Basic information

Entry
Database: PDB / ID: 7sc7
TitleSynechocystis PCC 6803 Phycobilisome core from up-down rod conformation
Components
  • (Allophycocyanin ...) x 4
  • (Phycobilisome ...) x 2
  • Phycobiliprotein ApcE
  • Sll1873 protein
KeywordsPHOTOSYNTHESIS / Complex / light harvesting / pigment
Function / homology
Function and homology information


Lyases / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / CpcD-like domain / CpcD/allophycocyanin linker domain ...Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Allophycocyanin subunit alpha-B / Phycobilisome rod-core linker polypeptide CpcG / Sll1873 protein / Allophycocyanin subunit beta-18 / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Allophycocyanin alpha chain / Allophycocyanin beta chain / Phycobiliprotein ApcE
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSauer, P.V. / Sutter, M. / Dominguez-Martin, M.A. / Kirst, H. / Kerfeld, C.A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN795070European Union
CitationJournal: Nature / Year: 2022
Title: Structures of a phycobilisome in light-harvesting and photoprotected states.
Authors: María Agustina Domínguez-Martín / Paul V Sauer / Henning Kirst / Markus Sutter / David Bína / Basil J Greber / Eva Nogales / Tomáš Polívka / Cheryl A Kerfeld /
Abstract: Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae. These large protein complexes capture incident sunlight and transfer the energy through a network of embedded ...Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae. 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. 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, 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.
History
DepositionSep 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 5, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Allophycocyanin alpha chain
AB: Allophycocyanin beta chain
AC: Allophycocyanin alpha chain
AD: Allophycocyanin beta chain
AE: Allophycocyanin subunit alpha-B
AF: Allophycocyanin beta chain
AH: Allophycocyanin alpha chain
AI: Allophycocyanin beta chain
AJ: Allophycocyanin alpha chain
AK: Allophycocyanin subunit beta-18
AL: Allophycocyanin beta chain
AN: Allophycocyanin alpha chain
AO: Allophycocyanin beta chain
AP: Allophycocyanin alpha chain
AQ: Allophycocyanin beta chain
AR: Allophycocyanin alpha chain
AS: Allophycocyanin beta chain
AU: Allophycocyanin beta chain
AV: Allophycocyanin alpha chain
AW: Allophycocyanin beta chain
AX: Allophycocyanin alpha chain
AY: Allophycocyanin beta chain
AZ: Allophycocyanin alpha chain
BA: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
BB: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
BD: Phycobiliprotein ApcE
BF: Phycobilisome rod-core linker polypeptide CpcG
BG: Sll1873 protein
BH: Allophycocyanin alpha chain
BI: Allophycocyanin beta chain
BJ: Allophycocyanin alpha chain
BK: Allophycocyanin beta chain
BL: Allophycocyanin subunit alpha-B
BM: Allophycocyanin beta chain
BO: Allophycocyanin alpha chain
BP: Allophycocyanin beta chain
BQ: Allophycocyanin alpha chain
BR: Allophycocyanin subunit beta-18
BS: Allophycocyanin beta chain
BU: Allophycocyanin alpha chain
BV: Allophycocyanin beta chain
BW: Allophycocyanin alpha chain
BX: Allophycocyanin beta chain
BY: Allophycocyanin alpha chain
BZ: Allophycocyanin beta chain
CB: Allophycocyanin alpha chain
CC: Allophycocyanin beta chain
CD: Allophycocyanin alpha chain
CE: Allophycocyanin beta chain
CF: Allophycocyanin alpha chain
CG: Allophycocyanin beta chain
CI: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
CJ: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
CL: Phycobiliprotein ApcE
CN: Phycobilisome rod-core linker polypeptide CpcG
CO: Sll1873 protein
CP: Allophycocyanin alpha chain
CQ: Allophycocyanin beta chain
CR: Allophycocyanin alpha chain
CS: Allophycocyanin beta chain
CT: Allophycocyanin alpha chain
CU: Allophycocyanin beta chain
CW: Allophycocyanin alpha chain
CX: Allophycocyanin beta chain
CY: Allophycocyanin alpha chain
CZ: Allophycocyanin beta chain
DA: Allophycocyanin alpha chain
DB: Allophycocyanin beta chain
DD: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
DE: Phycobilisome rod-core linker polypeptide CpcG
DF: Phycobilisome rod-core linker polypeptide CpcG
DG: Allophycocyanin alpha chain
DH: Allophycocyanin beta chain
DI: Allophycocyanin alpha chain
DJ: Allophycocyanin beta chain
DK: Allophycocyanin alpha chain
DL: Allophycocyanin beta chain
DN: Allophycocyanin alpha chain
DO: Allophycocyanin beta chain
DP: Allophycocyanin alpha chain
DQ: Allophycocyanin beta chain
DR: Allophycocyanin alpha chain
DS: Allophycocyanin beta chain
DU: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
DV: Phycobilisome rod-core linker polypeptide CpcG
DW: Phycobilisome rod-core linker polypeptide CpcG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,706,935158
Polymers1,664,54986
Non-polymers42,38672
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Allophycocyanin ... , 4 types, 70 molecules AAACAHAJANAPARAVAXAZBHBJBOBQBUBWBYCBCDCFCPCRCTCWCYDADGDIDKDN...

#1: Protein ...
Allophycocyanin alpha chain


Mass: 17429.807 Da / Num. of mol.: 32 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q01951
#2: Protein ...
Allophycocyanin beta chain


Mass: 17231.604 Da / Num. of mol.: 34 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q01952
#3: Protein Allophycocyanin subunit alpha-B /


Mass: 17940.393 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P72870
#4: Protein Allophycocyanin subunit beta-18 / / Allophycocyanin subunit B18


Mass: 18911.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P74551

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Phycobilisome ... , 2 types, 12 molecules BABBCICJDDDUBFCNDEDFDVDW

#5: Protein
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / LC 7.8


Mass: 7817.174 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q01950
#7: Protein
Phycobilisome rod-core linker polypeptide CpcG


Mass: 28938.758 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P73093

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Protein , 2 types, 4 molecules BDCLBGCO

#6: Protein Phycobiliprotein ApcE / Phycobilisome LCM core-membrane linker polypeptide / Phycobilisome core-membrane linker phycobiliprotein ApcE


Mass: 100412.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q55544, Lyases
#8: Protein Sll1873 protein


Mass: 12927.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P74135

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Non-polymers , 1 types, 72 molecules

#9: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Phycobilisome from Synechocystis PCC 6803 / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 3.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Details: Manual blotting

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20rc1_4392refinement
PHENIX1.20rc1_4392refinement
EM software
IDNameVersionCategory
1cryoSPARC3.1particle selection
2RELION3.1particle selection
3SerialEMimage acquisition
10PHENIX1.92model refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
14cryoSPARC3.13D reconstruction
Image processingDetails: Streptavidin lattice was subtracted after movie alignment.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 202719 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 133.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0042109592
ELECTRON MICROSCOPYf_angle_d0.8496148508
ELECTRON MICROSCOPYf_chiral_restr0.050616682
ELECTRON MICROSCOPYf_plane_restr0.006519044
ELECTRON MICROSCOPYf_dihedral_angle_d9.201916424

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