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- PDB-7efw: Crystal structure of hexameric state of C-phycocyanin from Thermo... -

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Basic information

Entry
Database: PDB / ID: 7efw
TitleCrystal structure of hexameric state of C-phycocyanin from Thermoleptolyngbya sp. O-77
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMinato, T. / Teramoto, T. / Hung, N.K. / Yamada, K. / Ogo, S. / Kakuta, Y. / Yoon, K.S.
Funding support Japan, 3items
OrganizationGrant numberCountry
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 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)224,82133
Polymers213,94812
Non-polymers10,87321
Water48,2082676
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60720 Å2
ΔGint-509 kcal/mol
Surface area67620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.089, 187.439, 210.065
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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 / Source: (natural) Leptolyngbya sp. O-77 (bacteria) / References: UniProt: A0A0X8WUE0
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2676 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 8% Tacsimate pH 5.0, 20 % Polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→49.2 Å / Num. obs: 264074 / % possible obs: 92.4 % / Redundancy: 5.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.083 / Rrim(I) all: 0.221 / Net I/σ(I): 8.6
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 2.9 % / Num. unique obs: 25606 / CC1/2: 0.495 / Rrim(I) all: 1.062 / % possible all: 65.1

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I7Y

1i7y


Resolution: 1.65→49.18 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1901 1999 -
Rwork0.1705 --
obs0.1706 264074 92.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14994 0 792 2676 18462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516469
X-RAY DIFFRACTIONf_angle_d0.9822498
X-RAY DIFFRACTIONf_dihedral_angle_d19.2276058
X-RAY DIFFRACTIONf_chiral_restr0.042479
X-RAY DIFFRACTIONf_plane_restr0.0042942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.2817890.250311641X-RAY DIFFRACTION58
1.69-1.740.23971050.232613771X-RAY DIFFRACTION69
1.74-1.790.26371230.220416098X-RAY DIFFRACTION80
1.79-1.850.22721400.208918329X-RAY DIFFRACTION91
1.85-1.910.24631490.192919563X-RAY DIFFRACTION98
1.91-1.990.24261530.179320103X-RAY DIFFRACTION100
1.99-2.080.19681540.174920094X-RAY DIFFRACTION100
2.08-2.190.1931530.166520092X-RAY DIFFRACTION100
2.19-2.330.18091540.163320154X-RAY DIFFRACTION100
2.33-2.50.18971530.166620208X-RAY DIFFRACTION100
2.5-2.760.16321550.166920229X-RAY DIFFRACTION100
2.76-3.160.17691560.165420326X-RAY DIFFRACTION100
3.16-3.980.17681560.151420467X-RAY DIFFRACTION100
3.98-49.180.16141590.156921000X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.1873 Å / Origin y: -45.0847 Å / Origin z: 21.8752 Å
111213212223313233
T0.1132 Å20.0006 Å20.001 Å2-0.1367 Å20.0076 Å2--0.1367 Å2
L-0.0026 °2-0.0034 °20.0198 °2-0.061 °2-0.0433 °2--0.0487 °2
S0.0138 Å °-0.0034 Å °-0.0142 Å °-0.0048 Å °-0.0064 Å °0.0095 Å °0.0217 Å °0.0051 Å °-0.0074 Å °
Refinement TLS groupSelection details: all

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