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- PDB-7veb: Phycocyanin rod structure of cyanobacterial phycobilisome -

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Basic information

Entry
Database: PDB / ID: 7veb
TitlePhycocyanin rod structure of cyanobacterial phycobilisome
Components
  • (C-phycocyanin ...) x 2
  • (Phycobilisome ...) x 3
KeywordsPHOTOSYNTHESIS / Phycobilisome / Phycocyanin rod / Light-harvesting
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. ...Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / C-phycocyanin alpha subunit / C-phycocyanin beta subunit / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod / Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod / Phycobilisome rod-core linker polypeptide CpcG2
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKawakami, K. / Hamaguchi, T. / Hirose, Y. / Kosumi, D. / Miyata, M. / Kamiya, N. / Yonekura, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H05109 Japan
Japan Society for the Promotion of Science (JSPS)20K06528 Japan
Japan Society for the Promotion of Science (JSPS)17H06434 Japan
CitationJournal: Nat Commun / Year: 2022
Title: Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome.
Authors: Keisuke Kawakami / Tasuku Hamaguchi / Yuu Hirose / Daisuke Kosumi / Makoto Miyata / Nobuo Kamiya / Koji Yonekura /
Abstract: Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are ...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.
History
DepositionSep 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-phycocyanin alpha subunit
B: C-phycocyanin beta subunit
C: C-phycocyanin alpha subunit
D: C-phycocyanin beta subunit
E: C-phycocyanin alpha subunit
F: C-phycocyanin beta subunit
G: C-phycocyanin alpha subunit
H: C-phycocyanin beta subunit
I: C-phycocyanin alpha subunit
J: C-phycocyanin beta subunit
K: C-phycocyanin alpha subunit
L: C-phycocyanin beta subunit
M: C-phycocyanin alpha subunit
N: C-phycocyanin beta subunit
O: C-phycocyanin alpha subunit
P: C-phycocyanin beta subunit
Q: C-phycocyanin alpha subunit
R: C-phycocyanin beta subunit
S: C-phycocyanin alpha subunit
T: C-phycocyanin beta subunit
U: C-phycocyanin alpha subunit
V: C-phycocyanin beta subunit
W: C-phycocyanin alpha subunit
X: C-phycocyanin beta subunit
Y: Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod
Z: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
a: Phycobilisome rod-core linker polypeptide CpcG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)518,93163
Polymers497,73827
Non-polymers21,19336
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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C-phycocyanin ... , 2 types, 24 molecules ACEGIKMOQSUWBDFHJLNPRTVX

#1: Protein
C-phycocyanin alpha subunit


Mass: 17456.631 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P50032
#2: Protein
C-phycocyanin beta subunit


Mass: 18216.652 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P50033

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Phycobilisome ... , 3 types, 3 molecules YZa

#3: Protein Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod / Rod-capping linker protein


Mass: 8681.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P50035
#4: Protein Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod


Mass: 32158.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P50034
#5: Protein Phycobilisome rod-core linker polypeptide CpcG2


Mass: 28817.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P50040

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Non-polymers , 1 types, 36 molecules

#6: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C33H40N4O6 / 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: Phycocyanin rod complex of cyanobacterial phyocobilisome
Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Thermosynechococcus vulcanus NIES-2134 (bacteria)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 150 µm
Image recordingElectron dose: 50.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7UCSF Chimera1.13model fitting
13PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 159537 / Symmetry type: POINT

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