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- PDB-8rk6: Baseplate core of bacteriophage JBD30 computed in C3 symmetry -

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Basic information

Entry
Database: PDB / ID: 8rk6
TitleBaseplate core of bacteriophage JBD30 computed in C3 symmetry
Components
  • DUF2163 domain-containing protein
  • Tip attachment protein J domain-containing protein
  • Virion structural protein
KeywordsVIRUS / Bacteriophage JBD30 / virion / baseplate core / baseplate upper protein / distal tail protein / baseplate hub protein
Function / homologyBacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / : / Bacteriophage phiJL001 Gp84 C-terminal domain-containing protein / Uncharacterized protein / Virion structural protein
Function and homology information
Biological speciesPseudomonas phage JBD30 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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
Citation
Journal: EMBO J / Year: 2024
Title: Structure and replication of Pseudomonas aeruginosa phage JBD30.
Authors: Lucie Valentová / Tibor Füzik / Jiří Nováček / Zuzana Hlavenková / Jakub Pospíšil / Pavel Plevka /
Abstract: Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection ...Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection cycle of the siphophage Casadabanvirus JBD30. Using its baseplate, JBD30 attaches to Pseudomonas aeruginosa via the bacterial type IV pilus, whose subsequent retraction brings the phage to the bacterial cell surface. Cryo-electron microscopy structures of the baseplate-pilus complex show that the tripod of baseplate receptor-binding proteins attaches to the outer bacterial membrane. The tripod and baseplate then open to release three copies of the tape-measure protein, an event that is followed by DNA ejection. JBD30 major capsid proteins assemble into procapsids, which expand by 7% in diameter upon filling with phage dsDNA. The DNA-filled heads are finally joined with 180-nm-long tails, which bend easily because flexible loops mediate contacts between the successive discs of major tail proteins. It is likely that the structural features and replication mechanisms described here are conserved among siphophages that utilize the type IV pili for initial cell attachment.
#1: Journal: 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
Revision 1.1Aug 28, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: DUF2163 domain-containing protein
C: Virion structural protein
M: Tip attachment protein J domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,0974
Polymers172,0413
Non-polymers561
Water00
1
I: DUF2163 domain-containing protein
C: Virion structural protein
M: Tip attachment protein J domain-containing protein
hetero molecules

I: DUF2163 domain-containing protein
C: Virion structural protein
M: Tip attachment protein J domain-containing protein
hetero molecules

I: DUF2163 domain-containing protein
C: Virion structural protein
M: Tip attachment protein J domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)516,29012
Polymers516,1239
Non-polymers1683
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
MethodUCSF CHIMERA

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Components

#1: Protein DUF2163 domain-containing protein


Mass: 29979.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P7M8
#2: Protein Virion structural protein


Mass: 62163.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P802
#3: Protein Tip attachment protein J domain-containing protein


Mass: 79898.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P7X4
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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
Details: Phage JBD30 was propagated in P. aeruginosa strain BAA-28 and purified using CsCl gradient.
Entity ID: #1-#3 / Source: NATURAL
Molecular weightValue: 0.516 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 MgSO4, 10 mM NaCl, 50 mM Tris pH 8
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
Specimen supportDetails: Gatan Solarus 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 force 0, blotting time 2 s, waiting time 15 s

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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
1EMAN22.91particle selection
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: 3.6 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: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00235709
ELECTRON MICROSCOPYf_angle_d0.47548783
ELECTRON MICROSCOPYf_dihedral_angle_d3.7265002
ELECTRON MICROSCOPYf_chiral_restr0.0445251
ELECTRON MICROSCOPYf_plane_restr0.0046410

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