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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: To Be Published
Title: Structure and quenching of a bundle-shaped phycobilisome
Authors: Burtseva, A.D. / Slonimskiy, Y.B. / Baymukhametov, T.N. / Sinetova, M.A. / Maksimov, E.G. / Popov, V.O. / Boyko, K.M. / Sluchanko, N.N.
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

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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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