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- PDB-9v7j: Phycobilisome core from Gloeobacter violaceus PCC 7421 -

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Basic information

Entry
Database: PDB / ID: 9v7j
TitlePhycobilisome core from Gloeobacter violaceus PCC 7421
Components
  • (Allophycocyanin ...) x 2
  • (Phycobilisome ...) x 2
  • Phycobiliprotein ApcE
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 / Phycobilisome core component / 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: 2.85 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
A: Phycobiliprotein ApcE
C: Phycobiliprotein ApcE
M: Allophycocyanin alpha subunit
N: Allophycocyanin beta subunit
O: Allophycocyanin alpha subunit
P: 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
Q: Allophycocyanin alpha subunit
R: Allophycocyanin beta subunit
S: Allophycocyanin alpha subunit
T: Allophycocyanin beta subunit
U: Allophycocyanin alpha subunit
V: Allophycocyanin beta subunit
W: Allophycocyanin alpha subunit
X: Allophycocyanin beta subunit
Y: Allophycocyanin alpha subunit
Z: Allophycocyanin beta subunit
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: Allophycocyanin alpha subunit
n: Allophycocyanin beta subunit
o: Allophycocyanin alpha subunit
p: Allophycocyanin beta subunit
q: Allophycocyanin beta subunit
r: Allophycocyanin alpha subunit
s: Phycobilisome core component
t: Allophycocyanin alpha subunit
u: Phycobilisome core component
v: Allophycocyanin beta subunit
w: Allophycocyanin alpha subunit
x: Allophycocyanin beta subunit
y: Allophycocyanin alpha subunit
z: Allophycocyanin beta subunit
1: Allophycocyanin alpha subunit
2: Allophycocyanin beta subunit
3: Allophycocyanin alpha subunit
4: Allophycocyanin beta subunit
5: Allophycocyanin alpha subunit
6: Allophycocyanin beta subunit
7: Allophycocyanin alpha subunit
8: Allophycocyanin beta subunit
9: Allophycocyanin alpha subunit
0: Allophycocyanin beta subunit
AA: Allophycocyanin alpha subunit
AB: Allophycocyanin beta subunit
AC: Allophycocyanin alpha subunit
AD: Allophycocyanin beta subunit
AE: Allophycocyanin alpha subunit
AF: Allophycocyanin beta subunit
AG: Allophycocyanin alpha subunit
AH: Allophycocyanin beta subunit
AI: Allophycocyanin alpha subunit
AJ: Allophycocyanin beta subunit
AK: Allophycocyanin alpha subunit
AL: Allophycocyanin beta subunit
AM: Allophycocyanin alpha subunit
AN: Allophycocyanin beta subunit
AO: Allophycocyanin alpha subunit
AP: Allophycocyanin beta subunit
AQ: Allophycocyanin alpha subunit
AR: Allophycocyanin beta subunit
AS: Allophycocyanin alpha subunit
AT: Allophycocyanin beta subunit
AU: Allophycocyanin alpha subunit
AV: Allophycocyanin beta subunit
AW: Allophycocyanin alpha subunit
AX: Allophycocyanin beta subunit
AY: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
AZ: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
Aa: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
Ab: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
Ac: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
Ad: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,782,820174
Polymers1,733,36990
Non-polymers49,45084
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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Allophycocyanin ... , 2 types, 80 molecules MOEGIKQSUWYacegikmortwy13579AAAC...

#2: Protein ...
Allophycocyanin alpha subunit


Mass: 17555.062 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL80
#3: Protein ...
Allophycocyanin beta subunit


Mass: 17241.664 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL79

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Phycobilisome ... , 2 types, 8 molecules suAYAZAaAbAcAd

#4: Protein Phycobilisome core component


Mass: 17452.838 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NJA2
#5: Protein
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core


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

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

#1: Protein Phycobiliprotein ApcE


Mass: 130002.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NL81
#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
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, #5 / 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 softwareName: REFMAC / Version: 5.8.0425 / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 746972 / Symmetry type: POINT

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