7EFW

Crystal structure of hexameric state of C-phycocyanin from Thermoleptolyngbya sp. O-77


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

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This is version 1.1 of the entry. See complete history


Literature

Non-conventional octameric structure of C-phycocyanin.

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.

(2021) Commun Biol 4: 1238-1238

  • DOI: https://doi.org/10.1038/s42003-021-02767-x
  • Primary Citation of Related Structures:  
    7EFV, 7EFW, 7EH7, 7EH8

  • PubMed 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 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.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin alpha chain
A, C, E, G, I
A, C, E, G, I, K
162Leptolyngbya sp. O-77Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin beta chain
B, D, F, H, J
B, D, F, H, J, L
172Leptolyngbya sp. O-77Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
AA [auth I]
BA [auth J]
CA [auth J]
EA [auth K]
FA [auth L]
AA [auth I],
BA [auth J],
CA [auth J],
EA [auth K],
FA [auth L],
GA [auth L],
M [auth A],
N [auth B],
O [auth B],
P [auth C],
Q [auth D],
R [auth D],
S [auth E],
V [auth F],
W [auth F],
X [auth G],
Y [auth H],
Z [auth H]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth J],
T [auth E],
U [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B, D, F, H, J
B, D, F, H, J, L
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.089α = 90
b = 187.439β = 90
c = 210.065γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJCR18R2
Japan Society for the Promotion of Science (JSPS)JapanJP18H02091
Japan Society for the Promotion of Science (JSPS)JapanJP18J00191

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description