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- PDB-7eh8: Cryo-EM structure of the hexameric state of C-phycocyanin from Th... -

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Basic information

Entry
Database: PDB / ID: 7eh8
TitleCryo-EM structure of the hexameric state of C-phycocyanin from Thermoleptolyngbya sp. O-77
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / homo hexamer / light-harvesting complex
Function / homology
Function and homology information


: / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, alpha subunit / Phycocyanin, beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / C-phycocyanin alpha chain / C-phycocyanin beta chain
Similarity search - Component
Biological speciesLeptolyngbya sp. O-77 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsMinato, T. / Teramoto, T. / Adachi, N. / Hung, N.K. / Yamada, K. / Kawasaki, M. / Akutsu, M. / Moriya, T. / Senda, T. / Ogo, S. ...Minato, T. / Teramoto, T. / Adachi, N. / Hung, N.K. / Yamada, K. / Kawasaki, M. / Akutsu, M. / Moriya, T. / Senda, T. / Ogo, S. / Kakuta, Y. / Yoon, K.S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20am0101071 Japan
Japan Science and TechnologyJPMJCR18R2 Japan
Japan Society for the Promotion of Science (JSPS)JP18H02091 Japan
Japan Society for the Promotion of Science (JSPS)JP18J00191 Japan
CitationJournal: Commun Biol / Year: 2021
Title: Non-conventional octameric structure of C-phycocyanin.
Authors: Takuo Minato / Takamasa Teramoto / Naruhiko Adachi / Nguyen Khac Hung / Kaho Yamada / Masato Kawasaki / Masato Akutsu / Toshio Moriya / Toshiya Senda / Seiji Ogo / Yoshimitsu Kakuta / Ki-Seok Yoon /
Abstract: C-phycocyanin (CPC), a blue pigment protein, is an indispensable component of giant phycobilisomes, which are light-harvesting antenna complexes in cyanobacteria that transfer energy efficiently to ...C-phycocyanin (CPC), a blue pigment protein, is an indispensable component of giant phycobilisomes, which are light-harvesting antenna complexes in cyanobacteria that transfer energy efficiently to photosystems I and II. X-ray crystallographic and electron microscopy (EM) analyses have revealed the structure of CPC to be a closed toroidal hexamer by assembling two trimers. In this study, the structural characterization of non-conventional octameric CPC is reported for the first time. Analyses of the crystal and cryogenic EM structures of the native CPC from filamentous thermophilic cyanobacterium Thermoleptolyngbya sp. O-77 unexpectedly illustrated the coexistence of conventional hexamer and novel octamer. In addition, an unusual dimeric state, observed via analytical ultracentrifugation, was postulated to be a key intermediate structure in the assemble of the previously unobserved octamer. These observations provide new insights into the assembly processes of CPCs and the mechanism of energy transfer in the light-harvesting complexes.
History
DepositionMar 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
C: C-phycocyanin alpha chain
D: C-phycocyanin beta chain
E: C-phycocyanin alpha chain
F: C-phycocyanin beta chain
G: C-phycocyanin alpha chain
H: C-phycocyanin beta chain
I: C-phycocyanin alpha chain
J: C-phycocyanin beta chain
K: C-phycocyanin alpha chain
L: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,54430
Polymers213,94812
Non-polymers10,59618
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
C-phycocyanin alpha chain


Mass: 17560.531 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Leptolyngbya sp. O-77 (bacteria) / References: UniProt: A0A0X8WU90
#2: Protein
C-phycocyanin beta chain


Mass: 18097.465 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: MEN: N-METHYL ASPARAGINE / Source: (natural) Leptolyngbya sp. O-77 (bacteria) / References: UniProt: A0A0X8WUE0
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
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: C-phycocyanin hexamer / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.22 MDa / Experimental value: NO
Source (natural)Organism: Leptolyngbya sp. O-77 (bacteria)
Buffer solutionpH: 7
SpecimenConc.: 6.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono-disperse.
Specimen supportDetails: The grid was washed by acetone prior to use. / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K / Details: Blotting time was 5 seconds (blot force 15)

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 49.2 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2036

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
7Cootmodel fitting
9PHENIXmodel refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 283980
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28120 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7EFW

7efw

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316026
ELECTRON MICROSCOPYf_angle_d1.0421796
ELECTRON MICROSCOPYf_dihedral_angle_d8.5652456
ELECTRON MICROSCOPYf_chiral_restr0.0372402
ELECTRON MICROSCOPYf_plane_restr0.0032833

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