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- PDB-7vea: Pentacylindrical allophycocyanin core from Thermosynechococcus vu... -

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Basic information

Entry
Database: PDB / ID: 7vea
TitlePentacylindrical allophycocyanin core from Thermosynechococcus vulcanus
Components
  • (Allophycocyanin ...) x 2
  • (Phycobilisome ...) x 2
  • Phycobiliprotein ApcE
KeywordsPHOTOSYNTHESIS / Light-harvesting complex / Phycobilisome / Energy transfer
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Allophycocyanin linker protein / Allophycocyanin linker chain / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. ...Allophycocyanin linker protein / Allophycocyanin linker chain / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / 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 / Allophycocyanin alpha chain / Allophycocyanin beta chain / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Phycobiliprotein ApcE / Phycobilisome core component
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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 22, 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
aA: Allophycocyanin alpha chain
aB: Allophycocyanin beta chain
aC: Allophycocyanin alpha chain
aD: Allophycocyanin beta chain
aE: Allophycocyanin alpha chain
aF: Allophycocyanin beta chain
aG: Allophycocyanin alpha chain
aH: Allophycocyanin beta chain
aI: Allophycocyanin alpha chain
aJ: Allophycocyanin beta chain
aK: Allophycocyanin alpha chain
aL: Allophycocyanin beta chain
aM: Phycobiliprotein ApcE
aN: Allophycocyanin beta chain
aO: Allophycocyanin alpha chain
aP: Allophycocyanin beta chain
aQ: Allophycocyanin alpha chain
aR: Phycobilisome core component
aS: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
bM: Allophycocyanin alpha chain
bN: Allophycocyanin beta chain
bO: Allophycocyanin alpha chain
bP: Allophycocyanin beta chain
bQ: Allophycocyanin alpha chain
bR: Allophycocyanin beta chain
bS: Allophycocyanin alpha chain
bT: Allophycocyanin beta chain
bU: Allophycocyanin alpha chain
bV: Allophycocyanin beta chain
bW: Allophycocyanin alpha chain
bX: Allophycocyanin beta chain
bY: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
cA: Allophycocyanin alpha chain
cB: Allophycocyanin beta chain
cC: Allophycocyanin alpha chain
cD: Allophycocyanin beta chain
cE: Allophycocyanin alpha chain
cF: Allophycocyanin beta chain
cG: Allophycocyanin alpha chain
cH: Allophycocyanin beta chain
cI: Allophycocyanin alpha chain
cJ: Allophycocyanin beta chain
cK: Allophycocyanin alpha chain
cL: Allophycocyanin beta chain
cM: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
dA: Allophycocyanin alpha chain
dB: Allophycocyanin beta chain
dC: Allophycocyanin alpha chain
dD: Allophycocyanin beta chain
dE: Allophycocyanin alpha chain
dF: Allophycocyanin beta chain
dG: Allophycocyanin alpha chain
dH: Allophycocyanin beta chain
dI: Allophycocyanin alpha chain
dJ: Allophycocyanin beta chain
dK: Allophycocyanin alpha chain
dL: Allophycocyanin beta chain
dM: Phycobiliprotein ApcE
dN: Allophycocyanin beta chain
dO: Allophycocyanin alpha chain
dP: Allophycocyanin beta chain
dQ: Allophycocyanin alpha chain
dR: Phycobilisome core component
dS: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
eM: Allophycocyanin alpha chain
eN: Allophycocyanin beta chain
eO: Allophycocyanin alpha chain
eP: Allophycocyanin beta chain
eQ: Allophycocyanin alpha chain
eR: Allophycocyanin beta chain
eS: Allophycocyanin alpha chain
eT: Allophycocyanin beta chain
eU: Allophycocyanin alpha chain
eV: Allophycocyanin beta chain
eW: Allophycocyanin alpha chain
eX: Allophycocyanin beta chain
eY: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
fA: Allophycocyanin alpha chain
fB: Allophycocyanin beta chain
fC: Allophycocyanin alpha chain
fD: Allophycocyanin beta chain
fE: Allophycocyanin alpha chain
fF: Allophycocyanin beta chain
fG: Allophycocyanin alpha chain
fH: Allophycocyanin beta chain
fI: Allophycocyanin alpha chain
fJ: Allophycocyanin beta chain
fK: Allophycocyanin alpha chain
fL: Allophycocyanin beta chain
fM: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,787,560174
Polymers1,738,11090
Non-polymers49,45084
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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Allophycocyanin ... , 2 types, 80 molecules aAaCaEaGaIaKaOaQbMbObQbSbUbWcAcCcEcGcIcKdAdCdEdGdIdKdOdQeMeO...

#1: Protein ...
Allophycocyanin alpha chain


Mass: 17555.926 Da / Num. of mol.: 40 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P50030
#2: Protein ...
Allophycocyanin beta chain


Mass: 17388.877 Da / Num. of mol.: 40 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P50031

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Phycobilisome ... , 2 types, 8 molecules aRdRaSbYcMdSeYfM

#4: Protein Phycobilisome core component


Mass: 18757.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: Q8DHC5
#5: Protein
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / LC 7.8


Mass: 7876.255 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: P50036

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Protein / Non-polymers , 2 types, 86 molecules aMdM

#3: Protein Phycobiliprotein ApcE


Mass: 127772.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: Q8DGF2
#6: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 84 / 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: Phycobilisome core complex from Thermosynechococcus vulcanus
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 / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 150 µm
Image recordingElectron dose: 84.1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20rc1_4387refinement
PHENIX1.20rc1_4387refinement
EM software
IDNameVersionCategory
7UCSF Chimera1.13model fitting
9PHENIX1.18.2model refinement
13RELION3.1.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25532 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 144.5 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033113126
ELECTRON MICROSCOPYf_angle_d0.6453154326
ELECTRON MICROSCOPYf_chiral_restr0.04417996
ELECTRON MICROSCOPYf_plane_restr0.003720222
ELECTRON MICROSCOPYf_dihedral_angle_d13.234537840

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