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- EMDB-2160: Electron cryo-microscopy of the empty (DNA-lacking) head of the y... -

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Entry
Database: EMDB / ID: EMD-2160
TitleElectron cryo-microscopy of the empty (DNA-lacking) head of the yersiniophage phiR1-37
Map dataThree-dimensional reconstruction of the empty (DNA-lacking) yersiniophage phiR1-37
Sample
  • Sample: Electron cryo-microscopy of the empty (DNA-lacking) head of the yersiniophage phiR1-37
  • Virus: Yersinia phage phiR1-37 (virus)
Keywordsvirus / Yersinia
Biological speciesYersinia phage phiR1-37 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 23.4 Å
AuthorsSkurnik M / Hyytiainen H / Happonen LJ / Kiljunen S / Datta N / Mattinen L / Williamson K / Kristo P / Szeliga M / Kalin-Manttari L ...Skurnik M / Hyytiainen H / Happonen LJ / Kiljunen S / Datta N / Mattinen L / Williamson K / Kristo P / Szeliga M / Kalin-Manttari L / Ahola-Iivarinen E / Kalkkinen N / Butcher SJ
CitationJournal: J Virol / Year: 2012
Title: Characterization of the genome, proteome, and structure of yersiniophage ϕR1-37.
Authors: Mikael Skurnik / Heidi J Hyytiäinen / Lotta J Happonen / Saija Kiljunen / Neeta Datta / Laura Mattinen / Kirsty Williamson / Paula Kristo / Magdalena Szeliga / Laura Kalin-Mänttäri / ...Authors: Mikael Skurnik / Heidi J Hyytiäinen / Lotta J Happonen / Saija Kiljunen / Neeta Datta / Laura Mattinen / Kirsty Williamson / Paula Kristo / Magdalena Szeliga / Laura Kalin-Mänttäri / Elina Ahola-Iivarinen / Nisse Kalkkinen / Sarah J Butcher /
Abstract: The bacteriophage vB_YecM-ϕR1-37 (ϕR1-37) is a lytic yersiniophage that can propagate naturally in different Yersinia species carrying the correct lipopolysaccharide receptor. This large-tailed ...The bacteriophage vB_YecM-ϕR1-37 (ϕR1-37) is a lytic yersiniophage that can propagate naturally in different Yersinia species carrying the correct lipopolysaccharide receptor. This large-tailed phage has deoxyuridine (dU) instead of thymidine in its DNA. In this study, we determined the genomic sequence of phage ϕR1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. The 262,391-bp genome of ϕR1-37 is one of the largest sequenced phage genomes, and it contains 367 putative open reading frames (ORFs) and 5 tRNA genes. Mass-spectrometric analysis identified 69 phage particle structural proteins with the genes scattered throughout the genome. A total of 269 of the ORFs (73%) lack homologues in sequence databases. Based on terminator and promoter sequences identified from the intergenic regions, the phage genome was predicted to consist of 40 to 60 transcriptional units. Image reconstruction revealed that the ϕR1-37 capsid consists of hexameric capsomers arranged on a T=27 lattice similar to the bacteriophage ϕKZ. The tail of ϕR1-37 has a contractile sheath. We conclude that phage ϕR1-37 is a representative of a novel phage type that carries the dU-containing genome in a ϕKZ-like head.
History
DepositionJul 9, 2012-
Header (metadata) releaseJul 25, 2012-
Map releaseOct 3, 2012-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 12000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 12000
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMDB-2160.jpg

Downloads & links

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Map

FileDownload / File: emd_2160.map.gz / Format: CCP4 / Size: 120.1 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationThree-dimensional reconstruction of the empty (DNA-lacking) yersiniophage phiR1-37
Voxel sizeX=Y=Z: 4.516 Å
Density
Contour LevelBy AUTHOR: 12000.0 / Movie #1: 12000
Minimum - Maximum-9828.0 - 32443.0
Average (Standard dev.)1.04251432 (±3679.423583979999876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions401401401
Spacing401401401
CellA=B=C: 1810.9159 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z4.5164.5164.516
M x/y/z401401401
origin x/y/z0.0000.0000.000
length x/y/z1810.9161810.9161810.916
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS401401401
D min/max/mean-9828.00032443.0001.043

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Supplemental data

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Sample components

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Entire : Electron cryo-microscopy of the empty (DNA-lacking) head of the y...

EntireName: Electron cryo-microscopy of the empty (DNA-lacking) head of the yersiniophage phiR1-37
Components
  • Sample: Electron cryo-microscopy of the empty (DNA-lacking) head of the yersiniophage phiR1-37
  • Virus: Yersinia phage phiR1-37 (virus)

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Supramolecule #1000: Electron cryo-microscopy of the empty (DNA-lacking) head of the y...

SupramoleculeName: Electron cryo-microscopy of the empty (DNA-lacking) head of the yersiniophage phiR1-37
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Yersinia phage phiR1-37

SupramoleculeName: Yersinia phage phiR1-37 / type: virus / ID: 1 / NCBI-ID: 331278 / Sci species name: Yersinia phage phiR1-37 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Yersinia enterocolitica (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 1380 Å / T number (triangulation number): 27

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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

BufferDetails: 50 mM Tris pH 7.8, 10 mM MgSO4
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 5.15 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 62000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
DetailsLow dose conditions
DateSep 7, 2009
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Number real images: 322 / Average electron dose: 15 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 23.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 1022

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