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- PDB-8to2: Bottom cylinder of high-resolution phycobilisome quenched by OCP ... -

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Basic information

Entry
Database: PDB / ID: 8to2
TitleBottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement)
Components
  • (Allophycocyanin ...) x 4
  • (Phycobilisome ...) x 2
  • Orange carotenoid-binding protein
  • Phycobiliprotein ApcE
  • Translation initiation factor IF-2
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 / Translation initiation factor IF-2 / Allophycocyanin subunit alpha-B / Phycobilisome rod-core linker polypeptide CpcG / Orange carotenoid-binding protein / Allophycocyanin subunit beta-18 / Allophycocyanin alpha chain / Allophycocyanin beta chain / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Phycobiliprotein ApcE
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å
AuthorsSauer, P.V. / Sutter, M. / Cupellini, L.
Funding supportEuropean Union, United States, Czech Republic, 4items
OrganizationGrant numberCountry
European Research Council (ERC)Grant ERC-AdG 786714 (LIFETimeS)European Union
Department of Energy (DOE, United States)DE-SC0020606 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127018 United States
Czech Science Foundation19-28323X Czech Republic
CitationJournal: Sci Adv / Year: 2024
Title: Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes.
Authors: Paul V Sauer / Lorenzo Cupellini / Markus Sutter / Mattia Bondanza / María Agustina Domínguez Martin / Henning Kirst / David Bína / Adrian Fujiet Koh / Abhay Kotecha / Basil J Greber / ...Authors: Paul V Sauer / Lorenzo Cupellini / Markus Sutter / Mattia Bondanza / María Agustina Domínguez Martin / Henning Kirst / David Bína / Adrian Fujiet Koh / Abhay Kotecha / Basil J Greber / Eva Nogales / Tomáš Polívka / Benedetta Mennucci / Cheryl A Kerfeld /
Abstract: Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) ...Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria.
History
DepositionAug 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phycobiliprotein ApcE
B: Orange carotenoid-binding protein
C: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
D: Allophycocyanin alpha chain
E: Allophycocyanin beta chain
F: Allophycocyanin alpha chain
G: Allophycocyanin beta chain
H: Allophycocyanin alpha chain
I: Allophycocyanin beta chain
J: Allophycocyanin alpha chain
K: Allophycocyanin beta chain
L: Allophycocyanin alpha chain
M: Allophycocyanin beta chain
N: Allophycocyanin alpha chain
O: Allophycocyanin beta chain
P: Phycobilisome rod-core linker polypeptide CpcG
c: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
d: Allophycocyanin subunit alpha-B
e: Allophycocyanin beta chain
f: Allophycocyanin alpha chain
g: Allophycocyanin beta chain
h: Allophycocyanin alpha chain
i: Allophycocyanin beta chain
j: Allophycocyanin alpha chain
k: Allophycocyanin beta chain
l: Allophycocyanin alpha chain
m: Allophycocyanin beta chain
o: Allophycocyanin subunit beta-18
p: Translation initiation factor IF-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)607,98954
Polymers593,29629
Non-polymers14,69325
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 3 molecules ABp

#1: Protein Phycobiliprotein ApcE


Mass: 100412.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55544
#2: Protein Orange carotenoid-binding protein


Mass: 34684.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74102
#9: Protein Translation initiation factor IF-2


Mass: 12927.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: A0A6P1VGS4

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Phycobilisome ... , 2 types, 3 molecules CcP

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


Mass: 7817.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q02925
#6: 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 (bacteria) / References: UniProt: P73093

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Allophycocyanin ... , 4 types, 23 molecules DFHJLNfhjlEGIKMOegikmdo

#4: Protein
Allophycocyanin alpha chain


Mass: 17429.807 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q01951
#5: Protein
Allophycocyanin beta chain


Mass: 17231.604 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q01952
#7: Protein Allophycocyanin subunit alpha-B /


Mass: 17940.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P72870
#8: Protein Allophycocyanin subunit beta-18 /


Mass: 18911.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74551

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Non-polymers , 2 types, 25 molecules

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


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


Mass: 564.840 Da / Num. of mol.: 1 / 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 bound to OCP
Type: COMPLEX / Entity ID: #1-#9 / 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
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: 1200 nm / Nominal defocus min: 400 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2particle selection
2EPUimage acquisition
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC4.23D reconstruction
Image processingDetails: Streptavidin lattice was subtracted after movie alignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153576 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 19.17 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003737772
ELECTRON MICROSCOPYf_angle_d0.639551196
ELECTRON MICROSCOPYf_chiral_restr0.05985733
ELECTRON MICROSCOPYf_plane_restr0.00497274
ELECTRON MICROSCOPYf_dihedral_angle_d5.43776138

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