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- EMDB-5717: The structure of Sinorhizobium meliloti phage phiM12, a novel T=1... -

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Basic information

Entry
Database: EMDB / ID: EMD-5717
TitleThe structure of Sinorhizobium meliloti phage phiM12, a novel T=19 icosahedral phage that is the founder of a new group of T4-like phages
Map dataCryo-EM reconstruction of phiM12, packed with DNA
Sample
  • Sample: T=19 icosahedral shell packed with DNA from phiM12, a bacteriophage of Sinorhizobium meliloti
  • Virus: Sinorhizobium phage phiM12 (virus)
Keywordsbacteriophage / phiM12 / Sinorhizobium meliloti / T=19 / rhizobia
Biological speciesSinorhizobium phage phiM12 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsStroupe ME / Brewer TE / Sousa DR / Jones KM
CitationJournal: Virology / Year: 2014
Title: The structure of Sinorhizobium meliloti phage ΦM12, which has a novel T=19l triangulation number and is the founder of a new group of T4-superfamily phages.
Authors: M Elizabeth Stroupe / Tess E Brewer / Duncan R Sousa / Kathryn M Jones /
Abstract: ΦM12 is the first example of a T=19l geometry capsid, encapsulating the recently sequenced genome. Here, we present structures determined by cryo-EM of full and empty capsids. The structure reveals ...ΦM12 is the first example of a T=19l geometry capsid, encapsulating the recently sequenced genome. Here, we present structures determined by cryo-EM of full and empty capsids. The structure reveals the pattern for assembly of 1140 HK97-like capsid proteins, pointing to interactions at the pseudo 3-fold symmetry axes that hold together the asymmetric unit. The particular smooth surface of the capsid, along with a lack of accessory coat proteins encoded by the genome, suggest that this interface is the primary mechanism for capsid assembly. Two-dimensional averages of the tail, including the neck and baseplate, reveal that ΦM12 has a relatively narrow neck that attaches the tail to the capsid, as well as a three-layer baseplate. When free from DNA, the icosahedral edges expand by about 5nm, while the vertices stay at the same position, forming a similarly smooth, but bowed, T=19l icosahedral capsid.
History
DepositionJul 11, 2013-
Header (metadata) releaseAug 21, 2013-
Map releaseApr 23, 2014-
UpdateApr 30, 2014-
Current statusApr 30, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0284
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0284
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5717.gif

Downloads & links

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Map

FileDownload / File: emd_5717.map.gz / Format: CCP4 / Size: 41.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of phiM12, packed with DNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.4 Å/pix.
x 224 pix.
= 1209.6 Å		5.4 Å/pix.
x 224 pix.
= 1209.6 Å		5.4 Å/pix.
x 224 pix.
= 1209.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.1 / Movie #1: 0.0284
Minimum - Maximum-0.06335218 - 0.28843483
Average (Standard dev.)0.04192379 (±0.09811363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 1209.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.45.45.4
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z1209.6001209.6001209.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0630.2880.042

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Supplemental data

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Sample components

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Entire : T=19 icosahedral shell packed with DNA from phiM12, a bacteriopha...

EntireName: T=19 icosahedral shell packed with DNA from phiM12, a bacteriophage of Sinorhizobium meliloti
Components
  • Sample: T=19 icosahedral shell packed with DNA from phiM12, a bacteriophage of Sinorhizobium meliloti
  • Virus: Sinorhizobium phage phiM12 (virus)

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Supramolecule #1000: T=19 icosahedral shell packed with DNA from phiM12, a bacteriopha...

SupramoleculeName: T=19 icosahedral shell packed with DNA from phiM12, a bacteriophage of Sinorhizobium meliloti
type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 2

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Supramolecule #1: Sinorhizobium phage phiM12

SupramoleculeName: Sinorhizobium phage phiM12 / type: virus / ID: 1 / NCBI-ID: 1357423 / Sci species name: Sinorhizobium phage phiM12 / Sci species strain: phiM12 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Sinorhizobium meliloti (bacteria) / Strain: 1021 / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: 1 / Diameter: 1000 Å / T number (triangulation number): 19

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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: 7 / Details: 10 mM Na2HPO4, 1 mM MgSO4
GridDetails: 200 mesh 2/2 Quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: blot 4 seconds

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateMay 13, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 1000 / Average electron dose: 15 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 65555 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsImages were selected by hand; initial model determined in EMAN and refined in EMAN and Frealign.
CTF correctionDetails: micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN, FREALIGN / Number images used: 2038

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