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- PDB-8rk3: Bacteriophage JBD30 baseplate - composite structure -

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Basic information

Entry
Database: PDB / ID: 8rk3
TitleBacteriophage JBD30 baseplate - composite structure
Components
  • (Virion structural ...) x 4
  • DUF2163 domain-containing protein
  • DUF2793 domain-containing protein
  • Tape measure protein N-terminal domain-containing protein
  • Tip attachment protein J domain-containing protein
KeywordsVIRUS / bacteriophage JBD30 / virion / baseplate
Function / homology
Function and homology information


Tape measure protein N-terminal / Tape measure protein / Protein of unknown function UCP028589 / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599
Similarity search - Domain/homology
Bacteriophage phiJL001 Gp84 C-terminal domain-containing protein / Virion structural protein / Virion structural protein / Uncharacterized protein / Virion structural protein / Virion structural protein / DUF2793 domain-containing protein / Tape measure protein N-terminal domain-containing protein
Similarity search - Component
Biological speciesPseudomonas phage JBD30 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.46 Å
AuthorsValentova, L. / Fuzik, T. / Plevka, P.
Funding support Czech Republic, European Union, 2items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLX22NPO5103 Czech Republic
European Research Council (ERC)101043452European Union
CitationJournal: Embo J. / Year: 2024
Title: Structure and replication of Pseudomonas aeruginosa phage JBD30
Authors: Valentova, L. / Plevka, P. / Fuzik, T. / Novacek, J. / Pospisil, J.
History
DepositionDec 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tape measure protein N-terminal domain-containing protein
B: Tape measure protein N-terminal domain-containing protein
C: Tape measure protein N-terminal domain-containing protein
g: DUF2163 domain-containing protein
U: Virion structural protein
a: DUF2793 domain-containing protein
W: DUF2793 domain-containing protein
e: DUF2793 domain-containing protein
o: Tip attachment protein J domain-containing protein
c: Virion structural protein
S: Virion structural protein
i: Virion structural protein
Y: Virion structural protein
k: Virion structural protein
m: Virion structural protein
q: Virion structural protein
s: Virion structural protein
O: DUF2163 domain-containing protein
r: Virion structural protein
I: DUF2793 domain-containing protein
E: DUF2793 domain-containing protein
M: DUF2793 domain-containing protein
b: Tip attachment protein J domain-containing protein
K: Virion structural protein
n: Virion structural protein
Q: Virion structural protein
G: Virion structural protein
T: Virion structural protein
X: Virion structural protein
f: Virion structural protein
j: Virion structural protein
P: DUF2163 domain-containing protein
D: Virion structural protein
J: DUF2793 domain-containing protein
F: DUF2793 domain-containing protein
N: DUF2793 domain-containing protein
d: Tip attachment protein J domain-containing protein
L: Virion structural protein
p: Virion structural protein
R: Virion structural protein
H: Virion structural protein
V: Virion structural protein
Z: Virion structural protein
h: Virion structural protein
l: Virion structural protein


Theoretical massNumber of molelcules
Total (without water)2,021,34945
Polymers2,021,34945
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 18 molecules ABCgOPaWeIEMJFNobd

#1: Protein Tape measure protein N-terminal domain-containing protein


Mass: 120920.586 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P847
#2: Protein DUF2163 domain-containing protein


Mass: 29979.053 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P7M8
#4: Protein
DUF2793 domain-containing protein


Mass: 40578.426 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P803
#5: Protein Tip attachment protein J domain-containing protein


Mass: 79898.781 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P7X4

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Virion structural ... , 4 types, 27 molecules UrDcikKQTLRVSYmnGXpHZqsfjhl

#3: Protein Virion structural protein


Mass: 62163.148 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P802
#6: Protein
Virion structural protein


Mass: 35014.137 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P7R6
#7: Protein
Virion structural protein


Mass: 33358.809 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P7X2
#8: Protein
Virion structural protein


Mass: 26983.729 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P801

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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: Pseudomonas phage JBD30 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.713 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Pseudomonas aeruginosa / Strain: BAA-28
Virus shellName: JBD30 capsid / Diameter: 640 nm / Triangulation number (T number): 7
Buffer solutionpH: 8 / Details: 10 mM NaCl, 10 mM MgSO4, 50 mM Tris-HCl
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMsodium chlorideNaCl1
210 mMmagnesium sulphateMgSO41
350 mMtris hydrochlorideTris-HCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: phage titer 10^11 PFU/ml
Specimen supportDetails: Gatan Solaris II / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: blotting time 2, blotting force 0, waiting time 5

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 34 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12356
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategoryDetails
2EPUimage acquisition
4Gctf1.06CTF correctionctf estimation
7Coot0.9.8.7model fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 8376
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1780 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL

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