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- EMDB-19270: Capsid of bacteriophage JBD30 decorated with minor capsid protein... -

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Basic information

Entry
Database: EMDB / ID: EMD-19270
TitleCapsid of bacteriophage JBD30 decorated with minor capsid protein trimers computed in I4 symmetry
Map datamain map
Sample
  • Virus: Pseudomonas phage JBD30 (virus)
    • Protein or peptide: Mu-like prophage FluMu N-terminal domain-containing protein
    • Protein or peptide: Bacteriophage Mu GpT domain-containing protein
Keywordsbacteriophage JBD30 / virion / capsid / minor capsid protein / major capsid protein / VIRUS
Function / homologyBacteriophage Mu, GpT / Mu-like prophage major head subunit gpT / Bacteriophage Mu GpT domain-containing protein / Mu-like prophage FluMu N-terminal domain-containing protein
Function and homology information
Biological speciesPseudomonas phage JBD30 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsValentova L / Fuzik T / Plevka P
Funding support Czech Republic, European Union, 2 items
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, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19270.png

Downloads & links

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Map

FileDownload / File: emd_19270.map.gz / Format: CCP4 / Size: 2.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.0027
Minimum - Maximum-0.009528606 - 0.016162418
Average (Standard dev.)0.000042841424 (±0.00059863576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-420-420-420
Dimensions840840840
Spacing840840840
CellA=B=C: 873.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19270_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pseudomonas phage JBD30

EntireName: Pseudomonas phage JBD30 (virus)
Components
  • Virus: Pseudomonas phage JBD30 (virus)
    • Protein or peptide: Mu-like prophage FluMu N-terminal domain-containing protein
    • Protein or peptide: Bacteriophage Mu GpT domain-containing protein

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Supramolecule #1: Pseudomonas phage JBD30

SupramoleculeName: Pseudomonas phage JBD30 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Phage JBD30 was propagated in P. aeruginosa strain BAA-28 and purified using CsCl gradient.
NCBI-ID: 1223260 / Sci species name: Pseudomonas phage JBD30 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: BAA-28
Molecular weightTheoretical: 19.052 MDa
Virus shellShell ID: 1 / Name: JBD30 capsid / Diameter: 640.0 Å / T number (triangulation number): 7

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Macromolecule #1: Mu-like prophage FluMu N-terminal domain-containing protein

MacromoleculeName: Mu-like prophage FluMu N-terminal domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 12.112113 KDa
SequenceString:
MARQNSAAKT TAKSKTDPAT EKPKDDTLPD STDDASPTAP ETPATKPDSA SDEVEGVFVR ATVERRCRAG FCFDKEGQGF ADGVLSDEQ LEALESDPLL KVERCTFSGN QEGE

UniProtKB: Mu-like prophage FluMu N-terminal domain-containing protein

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Macromolecule #2: Bacteriophage Mu GpT domain-containing protein

MacromoleculeName: Bacteriophage Mu GpT domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD30 (virus)
Molecular weightTheoretical: 33.69498 KDa
SequenceString: MAIITPALIS ALKTSFQKHF QDALATAPST YLQVATVIPS TTASNTYGWL GQFPKLREWI GQRVIKDMAA QGYQITNKLF ESTVGVKRT DIEDDNLGVY GPLMQEMGRA AGAHPDELVF ALLKAGNANL CYDGQNFFDT DHPVYPNVDG TGTATTVSNL F APAADPGA ...String:
MAIITPALIS ALKTSFQKHF QDALATAPST YLQVATVIPS TTASNTYGWL GQFPKLREWI GQRVIKDMAA QGYQITNKLF ESTVGVKRT DIEDDNLGVY GPLMQEMGRA AGAHPDELVF ALLKAGNANL CYDGQNFFDT DHPVYPNVDG TGTATTVSNL F APAADPGA AWYLLDTSRS LKPLIYQERM KPSFTSMTKE DDEQVFMADE YRYGVRSRCN VGFGFWQLAA MSTEELNQVN FE KVYDAMR NQKADGGRPL DIRPNLLVVP TTLRSKAKEV VGVQRLANGA DNPNFELVQV LDTAWLN

UniProtKB: Bacteriophage Mu GpT domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMNaClsodium chloride
10.0 mMMgSO4magnesium sulphate
50.0 mMTris-HClTris hydrochloride

Details: 10 mM MgSO4, 10 mM NaCl, 50 mM Tris pH 8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Details: Gatan Solarus II
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Detailsphage titer 10^11 PFU

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-25 / Number grids imaged: 1 / Number real images: 11300 / Average exposure time: 5.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 13129
Startup modelType of model: OTHER / Details: Stochastic gradient descent
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 5360
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8rkc:
Capsid of bacteriophage JBD30 decorated with minor capsid protein trimers computed in I4 symmetry

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