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- EMDB-5947: Bacteriophage CUS-3 capsid icosahedral reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-5947
TitleBacteriophage CUS-3 capsid icosahedral reconstruction
Map dataBacteriophage CUS-3 capsid icosahedral reconstruction
Sample
  • Sample: CUS-3 virion, icosahedrally averaged
  • Virus: Enterobacteria phage CUS-3 (virus)
Keywordsmature virion / capsid only / icosahedrally averaged
Biological speciesEnterobacteria phage CUS-3 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsParent KN / Tang J / Cardone G / Gilcrease EB / Janssen ME / Olson NH / Casjens SR / Baker TS
CitationJournal: Virology / Year: 2014
Title: Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain.
Authors: Kristin N Parent / Jinghua Tang / Giovanni Cardone / Eddie B Gilcrease / Mandy E Janssen / Norman H Olson / Sherwood R Casjens / Timothy S Baker /
Abstract: CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions ...CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the "HK97-fold" shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain ("I-domain"), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently.
History
DepositionApr 16, 2014-
Header (metadata) releaseJul 30, 2014-
Map releaseJul 30, 2014-
UpdateAug 27, 2014-
Current statusAug 27, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8240
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 8240
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5947.png

Downloads & links

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Map

FileDownload / File: emd_5947.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage CUS-3 capsid icosahedral reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 801 pix.
= 1081.35 Å		1.35 Å/pix.
x 801 pix.
= 1081.35 Å		1.35 Å/pix.
x 801 pix.
= 1081.35 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8240.0 / Movie #1: 8240
Minimum - Maximum-15582.0 - 32443.0
Average (Standard dev.)-116.158798219999994 (±2034.53149413999995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions801801801
Spacing801801801
CellA=B=C: 1081.35 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z801801801
origin x/y/z0.0000.0000.000
length x/y/z1081.3501081.3501081.350
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-400-400-400
NC/NR/NS801801801
D min/max/mean-15582.00032443.000-116.159

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Supplemental data

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Sample components

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Entire : CUS-3 virion, icosahedrally averaged

EntireName: CUS-3 virion, icosahedrally averaged
Components
  • Sample: CUS-3 virion, icosahedrally averaged
  • Virus: Enterobacteria phage CUS-3 (virus)

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Supramolecule #1000: CUS-3 virion, icosahedrally averaged

SupramoleculeName: CUS-3 virion, icosahedrally averaged / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1

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Supramolecule #1: Enterobacteria phage CUS-3

SupramoleculeName: Enterobacteria phage CUS-3 / type: virus / ID: 1 / NCBI-ID: 539221 / Sci species name: Enterobacteria phage CUS-3 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli) / Strain: K1 / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: capsid / Diameter: 690 Å / T number (triangulation number): 7

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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

Concentration10 mg/mL
BufferpH: 7.6 / Details: 10 mM Tris, 10 mM MgCl2
GridDetails: 400 mesh R2/2 Quantifoil, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 5 sec before plunging.

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 89 K / Max: 91 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at the magnification used to collect data.
DateSep 1, 2013
Image recordingCategory: CCD / Film or detector model: DIRECT ELECTRON DE-12 (4k x 3k) / Digitization - Sampling interval: 6 µm / Number real images: 419 / Average electron dose: 23 e/Å2
Details: The data were collected on the DE12 camera under control of the automated acquisition software, LEGINON.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 4.08 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 31000
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsAuto3dem was used for refinement.
CTF correctionDetails: each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: OTHER / Software - Name: Auto3dem, RobEM, autopp
Details: 28 frames total were collected for each image (35 e-/A2 total dose). Only 15 were used in the final reconstruction (18e-/A2 dose).
Number images used: 7766

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