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- PDB-7scc: T-cylinder of Synechocystis PCC 6803 Phycobilisome, complex with ... -

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Basic information

Entry
Database: PDB / ID: 7scc
TitleT-cylinder of Synechocystis PCC 6803 Phycobilisome, complex with OCP - local refinement
Components
  • (Allophycocyanin ...) x 2
  • (Phycobilisome ...) x 2
  • Orange carotenoid-binding protein
  • Phycobiliprotein ApcE
KeywordsPHOTOSYNTHESIS / Complex / light harvesting / pigment
Function / homology
Function and homology information


light absorption / Lyases / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / photoreceptor activity / photosynthesis / lyase activity
Similarity search - Function
Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Orange carotenoid-binding protein, N-terminal / Orange carotenoid-binding protein, N-terminal domain superfamily / Orange carotenoid protein, N-terminal / Orange carotenoid protein (OCP) N-terminal domain profile. / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily ...Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Orange carotenoid-binding protein, N-terminal / Orange carotenoid-binding protein, N-terminal domain superfamily / Orange carotenoid protein, N-terminal / Orange carotenoid protein (OCP) N-terminal domain profile. / 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 / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / NTF2-like domain superfamily / Globin-like superfamily
Similarity search - Domain/homology
beta,beta-carotene-4,4'-dione / PHYCOCYANOBILIN / Phycobilisome rod-core linker polypeptide CpcG / Orange carotenoid-binding protein / 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: 2.6 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 alpha chain
AF: Allophycocyanin beta chain
AH: Allophycocyanin alpha chain
AI: Allophycocyanin beta chain
AJ: Allophycocyanin alpha chain
AK: Allophycocyanin beta chain
AL: Allophycocyanin alpha chain
AM: Allophycocyanin beta chain
AO: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
AQ: Phycobiliprotein ApcE
AS: Orange carotenoid-binding protein
AT: Orange carotenoid-binding protein
AU: Phycobilisome rod-core linker polypeptide CpcG
AV: Phycobilisome rod-core linker polypeptide CpcG
AW: Allophycocyanin alpha chain
AX: Allophycocyanin beta chain
AY: Allophycocyanin alpha chain
AZ: Allophycocyanin beta chain
BA: Allophycocyanin alpha chain
BB: Allophycocyanin beta chain
BD: Allophycocyanin alpha chain
BE: Allophycocyanin beta chain
BF: Allophycocyanin alpha chain
BG: Allophycocyanin beta chain
BH: Allophycocyanin alpha chain
BI: Allophycocyanin beta chain
BK: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
BM: Phycobiliprotein ApcE
BO: Orange carotenoid-binding protein
BP: Orange carotenoid-binding protein
BQ: Phycobilisome rod-core linker polypeptide CpcG
BR: Phycobilisome rod-core linker polypeptide CpcG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)902,14862
Polymers886,89036
Non-polymers15,25826
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 ... , 2 types, 24 molecules AAACAEAHAJALAWAYBABDBFBHABADAFAIAKAMAXAZBBBEBGBI

#1: Protein
Allophycocyanin alpha chain


Mass: 17429.807 Da / Num. of mol.: 12 / 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.: 12 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q01952

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Phycobilisome ... , 2 types, 6 molecules AOBKAUAVBQBR

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


Mass: 7817.174 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: Q01950
#6: Protein
Phycobilisome rod-core linker polypeptide CpcG


Mass: 28938.758 Da / Num. of mol.: 4 / 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, 6 molecules AQBMASATBOBP

#4: 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
#5: Protein
Orange carotenoid-binding protein / OCP


Mass: 34684.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa / Gene: slr1963 / Production host: Escherichia coli (E. coli) / References: UniProt: P74102

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Non-polymers , 2 types, 26 molecules

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


Mass: 588.694 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin / Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H52O2 / 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: Complex of phycobilisome from Synechocystis PCC 6803 with OCP
Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES
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 FIELDBright-field microscopy / Nominal defocus max: 1600 nm / Nominal defocus min: 500 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
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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176804 / Symmetry type: POINT
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 113.47 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001743584
ELECTRON MICROSCOPYf_angle_d0.423759090
ELECTRON MICROSCOPYf_chiral_restr0.03466668
ELECTRON MICROSCOPYf_plane_restr0.00297602
ELECTRON MICROSCOPYf_dihedral_angle_d7.43766444

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