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- PDB-9v7k: Phycobilisome allophycocyanin hexamer C from Gloeobacter violaceu... -

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Basic information

Entry
Database: PDB / ID: 9v7k
TitlePhycobilisome allophycocyanin hexamer C from Gloeobacter violaceus PCC 7421
Components
  • (Allophycocyanin ...) x 2
  • Glr1262 protein
  • Glr2806 protein
  • Phycobiliprotein ApcE
  • Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
KeywordsPHOTOSYNTHESIS / Phycobilisome
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 / Glr2806 protein / Glr1262 protein / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Allophycocyanin beta subunit / Allophycocyanin alpha subunit / Phycobiliprotein ApcE
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsBurtseva, A.D. / Baymukhametov, T.N. / Slonimskiy, Y.B. / Popov, V.O. / Sluchanko, N.N. / Boyko, K.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-74-00062 Russian Federation
CitationJournal: Sci Adv / Year: 2025
Title: Structure and quenching of a bundle-shaped phycobilisome.
Authors: Anna D Burtseva / Yury B Slonimskiy / Timur N Baymukhametov / Maria A Sinetova / Daniil A Gvozdev / Georgy V Tsoraev / Dmitry A Cherepanov / Eugene G Maksimov / Vladimir O Popov / Konstantin ...Authors: Anna D Burtseva / Yury B Slonimskiy / Timur N Baymukhametov / Maria A Sinetova / Daniil A Gvozdev / Georgy V Tsoraev / Dmitry A Cherepanov / Eugene G Maksimov / Vladimir O Popov / Konstantin M Boyko / Nikolai N Sluchanko /
Abstract: Cyanobacteria use soluble antenna megacomplexes, phycobilisomes (PBSs), to maximize light-harvesting efficiency and small photoswitchable orange carotenoid proteins (OCPs) to down-regulate PBSs in ...Cyanobacteria use soluble antenna megacomplexes, phycobilisomes (PBSs), to maximize light-harvesting efficiency and small photoswitchable orange carotenoid proteins (OCPs) to down-regulate PBSs in high light. Among known PBS morphologies, the one from the basal cyanobacterial genus still lacks detailed structural characterization. Here, we reconstructed a cryo-electron microscopy structure of the >10-megadalton PBS, with diverging, conformationally mobile bundles of rods composed of stacked phycoerythrin and phycocyanin hexamers, stemming from a pentacylindrical allophycocyanin core belted by auxiliary phycocyanin hexamers. We show how two -specific multidomain linker proteins, Glr1262 and Glr2806, maintain this bundle-shaped architecture and reveal its differential regulation via nonphotochemical quenching by two OCP types of that recognize separate binding sites within the allophycocyanin core, including lateral cylinders absent in tricylindrical cores.
History
DepositionMay 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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 / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Phycobiliprotein ApcE
Z: Glr1262 protein
A: Allophycocyanin alpha subunit
B: Allophycocyanin beta subunit
C: Allophycocyanin alpha subunit
D: Allophycocyanin beta subunit
E: Allophycocyanin alpha subunit
F: Allophycocyanin beta subunit
G: Allophycocyanin alpha subunit
H: Allophycocyanin beta subunit
I: Allophycocyanin alpha subunit
J: Allophycocyanin beta subunit
K: Allophycocyanin alpha subunit
L: Allophycocyanin beta subunit
M: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
X: Glr2806 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)527,28428
Polymers520,22016
Non-polymers7,06412
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 4 molecules 1ZMX

#1: Protein Phycobiliprotein ApcE


Mass: 130002.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL81
#2: Protein Glr1262 protein


Mass: 92127.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL64
#5: Protein Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core


Mass: 7765.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL78
#6: Protein Glr2806 protein


Mass: 81544.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NGT2

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Allophycocyanin ... , 2 types, 12 molecules ACEGIKBDFHJL

#3: Protein
Allophycocyanin alpha subunit


Mass: 17555.062 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL80
#4: Protein
Allophycocyanin beta subunit


Mass: 17241.664 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL79

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Non-polymers , 1 types, 12 molecules

#7: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: Bundle-shaped phycobilisome / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Buffer solutionpH: 7
Buffer componentConc.: 50 mM / Name: Tris(hydroxymethyl)aminomethane hydrochloride / Formula: Tris-HCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: Preliminary grid screening was performed manually.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 85000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 0.01 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.9 sec. / Electron dose: 66 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Spherical aberration corrector: Microscope was modified with a Cs corrector (CEOS GmbH, Germany).
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
2SerialEM4.04image acquisition
4Warp1.0.9CTF correction
11cryoSPARC4.7final Euler assignment
13cryoSPARC4.73D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 746972 / Symmetry type: POINT

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