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- EMDB-8488: Bacteriophage PAU -

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Basic information

Entry
Database: EMDB / ID: EMD-8488
TitleBacteriophage PAU
Map dataBacteriophage PAU
Sample
  • Virus: bacteriophage PAU (virus)
Biological speciesbacteriophage PAU (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsHua J / Huet A / Lopez CA / Toropova K / Pope WH / Duda RL / Hendrix RW / Conway JF
Funding support United States, 4 items
OrganizationGrant numberCountry
Commonwealth of PennsylvaniaSAP 4100031302 United States
National Science Foundation (NSF, United States)1050750 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM047795 United States
National Institutes of Health/Office of the DirectorS10 OD019995 United States
CitationJournal: mBio / Year: 2017
Title: Capsids and Genomes of Jumbo-Sized Bacteriophages Reveal the Evolutionary Reach of the HK97 Fold.
Authors: Jianfei Hua / Alexis Huet / Carlos A Lopez / Katerina Toropova / Welkin H Pope / Robert L Duda / Roger W Hendrix / James F Conway /
Abstract: Large icosahedral viruses that infect bacteria represent an extreme of the coevolution of capsids and the genomes they accommodate. One subset of these large viruses is the jumbophages, tailed phages ...Large icosahedral viruses that infect bacteria represent an extreme of the coevolution of capsids and the genomes they accommodate. One subset of these large viruses is the jumbophages, tailed phages with double-stranded DNA genomes of at least 200,000 bp. We explored the mechanism leading to increased capsid and genome sizes by characterizing structures of several jumbophage capsids and the DNA packaged within them. Capsid structures determined for six jumbophages were consistent with the canonical phage HK97 fold, and three had capsid geometries with novel triangulation numbers (T=25, T=28, and T=52). Packaged DNA (chromosome) sizes were larger than the genome sizes, indicating that all jumbophages use a head-full DNA packaging mechanism. For two phages (PAU and G), the sizes appeared very much larger than their genome length. We used two-dimensional DNA gel electrophoresis to show that these two DNAs migrated abnormally due to base modifications and to allow us to calculate their actual chromosome sizes. Our results support a ratchet model of capsid and genome coevolution whereby mutations lead to increased capsid volume and allow the acquisition of additional genes. Once the added genes and larger capsid are established, mutations that restore the smaller size are disfavored. A large family of viruses share the same fold of the capsid protein as bacteriophage HK97, a virus that infects bacteria. Members of this family use different numbers of the capsid protein to build capsids of different sizes. Here, we examined the structures of extremely large capsids and measured their DNA content relative to the sequenced genome lengths, aiming to understand the process that increases size. We concluded that mutational changes leading to larger capsids become locked in by subsequent changes to the genome organization.
History
DepositionNov 29, 2016-
Header (metadata) releaseFeb 8, 2017-
Map releaseNov 1, 2017-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8488.png

Downloads & links

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Map

FileDownload / File: emd_8488.map.gz / Format: CCP4 / Size: 340.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage PAU
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.26 Å/pix.
x 447 pix.
= 1457.22 Å		3.26 Å/pix.
x 447 pix.
= 1457.22 Å		3.26 Å/pix.
x 447 pix.
= 1457.22 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6 / Movie #1: 6
Minimum - Maximum-11.3698 - 25.197752
Average (Standard dev.)0.21042891 (±2.2242575)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions447447447
Spacing447447447
CellA=B=C: 1457.22 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.263.263.26
M x/y/z447447447
origin x/y/z0.0000.0000.000
length x/y/z1457.2201457.2201457.220
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS447447447
D min/max/mean-11.37025.1980.210

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Supplemental data

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Sample components

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Entire : bacteriophage PAU

EntireName: bacteriophage PAU (virus)
Components
  • Virus: bacteriophage PAU (virus)

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Supramolecule #1: bacteriophage PAU

SupramoleculeName: bacteriophage PAU / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 115992 / Sci species name: bacteriophage PAU / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Sphingomonas paucimobilis (bacteria)
Virus shellShell ID: 1 / Name: capsid / Diameter: 1120.0 Å / T number (triangulation number): 25

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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

Concentration1 mg/mL
BufferpH: 7.9
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
10.0 mMMgSO4magnesium chloride
GridMaterial: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 6.35 µm / Number real images: 177 / Average exposure time: 2.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 38000
Sample stageSpecimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10348
CTF correctionSoftware - Name: CTFFIND3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3DEM / Number images used: 9260
Initial angle assignmentType: COMMON LINE / Software - Name: Auto3DEM
Final angle assignmentType: COMMON LINE / Software - Name: Auto3DEM
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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