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- PDB-7sc8: Synechocystis PCC 6803 Phycobilisome rod from PBS sample -

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Basic information

Entry
Database: PDB / ID: 7sc8
TitleSynechocystis PCC 6803 Phycobilisome rod from PBS sample
Components
  • (C-phycocyanin ...) x 2
  • (Phycobilisome ...) x 4
KeywordsPHOTOSYNTHESIS / Complex / light harvesting / pigment
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. ...Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / 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 / Phycobilisome rod-core linker polypeptide CpcG / Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1 / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 / C-phycocyanin beta subunit / C-phycocyanin alpha subunit
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 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
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: C-phycocyanin alpha subunit
AB: C-phycocyanin beta subunit
AC: C-phycocyanin alpha subunit
AD: C-phycocyanin beta subunit
AE: C-phycocyanin alpha subunit
AF: C-phycocyanin beta subunit
AG: C-phycocyanin alpha subunit
AH: C-phycocyanin beta subunit
AI: C-phycocyanin alpha subunit
AJ: C-phycocyanin beta subunit
AK: C-phycocyanin alpha subunit
AL: C-phycocyanin beta subunit
AM: C-phycocyanin alpha subunit
AN: C-phycocyanin beta subunit
AO: C-phycocyanin alpha subunit
AP: C-phycocyanin beta subunit
AQ: C-phycocyanin alpha subunit
AR: C-phycocyanin beta subunit
AS: C-phycocyanin alpha subunit
AT: C-phycocyanin beta subunit
AU: C-phycocyanin alpha subunit
AV: C-phycocyanin beta subunit
AW: C-phycocyanin alpha subunit
AX: C-phycocyanin beta subunit
AY: C-phycocyanin alpha subunit
AZ: C-phycocyanin beta subunit
BA: C-phycocyanin alpha subunit
BB: C-phycocyanin beta subunit
BC: C-phycocyanin alpha subunit
BD: C-phycocyanin beta subunit
BE: C-phycocyanin alpha subunit
BF: C-phycocyanin beta subunit
BG: C-phycocyanin alpha subunit
BH: C-phycocyanin beta subunit
BI: C-phycocyanin alpha subunit
BJ: C-phycocyanin beta subunit
BK: Phycobilisome rod-core linker polypeptide CpcG
BL: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1
BM: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2
BN: Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod
hetero molecules


Theoretical massNumber of molelcules
Total (without water)776,86694
Polymers745,07640
Non-polymers31,78954
Water48,1362672
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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C-phycocyanin ... , 2 types, 36 molecules AAACAEAGAIAKAMAOAQASAUAWAYBABCBEBGBIABADAFAHAJALANAPARATAVAX...

#1: Protein
C-phycocyanin alpha subunit


Mass: 17602.529 Da / Num. of mol.: 18 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q54715
#2: Protein
C-phycocyanin beta subunit


Mass: 18142.426 Da / Num. of mol.: 18 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q54714

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Phycobilisome ... , 4 types, 4 molecules BKBLBMBN

#3: Protein Phycobilisome rod-core linker polypeptide CpcG


Mass: 28938.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P73093
#4: Protein Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1


Mass: 32558.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P73203
#5: Protein Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 / LR30


Mass: 30836.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P73204
#6: Protein Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod / L-8.9/R / Rod-capping linker protein


Mass: 9333.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P73202

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Non-polymers , 2 types, 2726 molecules

#7: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2672 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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-#6 / 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 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 FIELD / 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_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
9PHENIX1.92model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3.13D reconstruction
Image processingDetails: Streptavidin lattice was subtracted after movie alignment.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2102860 / 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: 16.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007455030
ELECTRON MICROSCOPYf_angle_d1.045774854
ELECTRON MICROSCOPYf_chiral_restr0.06558181
ELECTRON MICROSCOPYf_plane_restr0.008411371
ELECTRON MICROSCOPYf_dihedral_angle_d17.050620848

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