7VEB

Phycocyanin rod structure of cyanobacterial phycobilisome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome.

Kawakami, K.Hamaguchi, T.Hirose, Y.Kosumi, D.Miyata, M.Kamiya, N.Yonekura, K.

(2022) Nat Commun 13: 3389-3389

  • DOI: https://doi.org/10.1038/s41467-022-30962-9
  • Primary Citation of Related Structures:  
    7VEA, 7VEB

  • PubMed Abstract: 

    Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are compositionally and structurally diverse, and exceedingly complex, all of which pose a challenge for a comprehensive understanding of their function. To date, three detailed architectures of PBSs by cryo-electron microscopy (cryo-EM) have been described: a hemiellipsoidal type, a block-type from rhodophytes, and a cyanobacterial hemidiscoidal-type. Here, we report cryo-EM structures of a pentacylindrical allophycocyanin core and phycocyanin-containing rod of a thermophilic cyanobacterial hemidiscoidal PBS. The structures define the spatial arrangement of protein subunits and chromophores, crucial for deciphering the energy transfer mechanism. They reveal how the pentacylindrical core is formed, identify key interactions between linker proteins and the bilin chromophores, and indicate pathways for unidirectional energy transfer.


  • Organizational Affiliation

    Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1, Sayo, Hyogo, 679-5148, Japan. kawakami.k@spring8.or.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin alpha subunit
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S, U, W
162Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P50032 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P50032 
Go to UniProtKB:  P50032
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50032
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin beta subunit
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
172Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P50033 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Go to UniProtKB:  P50033
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50033
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod78Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P50035 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P50035 
Go to UniProtKB:  P50035
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50035
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod287Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P50034 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P50034 
Go to UniProtKB:  P50034
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50034
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome rod-core linker polypeptide CpcG2AA [auth a]246Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P50040 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P50040 
Go to UniProtKB:  P50040
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UniProt GroupP50040
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
AB [auth R]
BA [auth A]
BB [auth R]
CA [auth B]
CB [auth S]
AB [auth R],
BA [auth A],
BB [auth R],
CA [auth B],
CB [auth S],
DA [auth B],
DB [auth T],
EA [auth C],
EB [auth T],
FA [auth D],
FB [auth U],
GA [auth D],
GB [auth V],
HA [auth E],
HB [auth V],
IA [auth F],
IB [auth W],
JA [auth F],
JB [auth X],
KA [auth G],
KB [auth X],
LA [auth H],
MA [auth H],
NA [auth I],
OA [auth J],
PA [auth J],
QA [auth K],
RA [auth L],
SA [auth L],
TA [auth M],
UA [auth N],
VA [auth N],
WA [auth O],
XA [auth P],
YA [auth P],
ZA [auth Q]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan20H05109
Japan Society for the Promotion of Science (JSPS)Japan20K06528
Japan Society for the Promotion of Science (JSPS)Japan17H06434

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-08-17
    Changes: Database references