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- EMDB-2365: Asymmetric structure of a virus-receptor complex -

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Basic information

Entry
Database: EMDB / ID: EMD-2365
TitleAsymmetric structure of a virus-receptor complex
Map dataSub-tomogram average of bacteriophage MS2 bound to its receptor
Sample
  • Sample: Bacteriophage MS2 bound to its receptor, the E. coli F-pilus
  • Virus: Enterobacterio phage MS2 (virus)
  • Organelle or cellular component: F-Pilus
Keywordsvirus / receptor / complex / asymmetric / bacteriophage
Function / homology
Function and homology information


negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli) / Enterobacterio phage MS2 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 39.0 Å
AuthorsDent KC / Thompson R / Barker AM / Barr JN / Hiscox JA / Stockley PG / Ranson NA
CitationJournal: Structure / Year: 2013
Title: The asymmetric structure of an icosahedral virus bound to its receptor suggests a mechanism for genome release.
Authors: Kyle C Dent / Rebecca Thompson / Amy M Barker / Julian A Hiscox / John N Barr / Peter G Stockley / Neil A Ranson /
Abstract: Simple, spherical RNA viruses have well-understood, symmetric protein capsids, but little structural information is available for their asymmetric components, such as minor proteins and their ...Simple, spherical RNA viruses have well-understood, symmetric protein capsids, but little structural information is available for their asymmetric components, such as minor proteins and their genomes, which are vital for infection. Here, we report an asymmetric structure of bacteriophage MS2, attached to its receptor, the F-pilus. Cryo-electron tomography and subtomographic averaging of such complexes result in a structure containing clear density for the packaged genome, implying that the conformation of the genome is the same in each virus particle. The data also suggest that the single-copy viral maturation protein breaks the symmetry of the capsid, occupying a position that would be filled by a coat protein dimer in an icosahedral shell. This capsomere can thus fulfill its known biological roles in receptor and genome binding and suggests an exit route for the genome during infection.
History
DepositionApr 18, 2013-
Header (metadata) releaseApr 24, 2013-
Map releaseJul 17, 2013-
UpdateSep 4, 2013-
Current statusSep 4, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4bp7
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4bp7
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2365.png

Downloads & links

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Map

FileDownload / File: emd_2365.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram average of bacteriophage MS2 bound to its receptor
Voxel sizeX=Y=Z: 9.12 Å
Density
Contour LevelBy AUTHOR: 1.45 / Movie #1: 1.3
Minimum - Maximum-3.95017767 - 7.49030733
Average (Standard dev.)0.00000759 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 583.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.129.129.12
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z583.680583.680583.680
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-3.9507.4900.000

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Supplemental data

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Sample components

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Entire : Bacteriophage MS2 bound to its receptor, the E. coli F-pilus

EntireName: Bacteriophage MS2 bound to its receptor, the E. coli F-pilus
Components
  • Sample: Bacteriophage MS2 bound to its receptor, the E. coli F-pilus
  • Virus: Enterobacterio phage MS2 (virus)
  • Organelle or cellular component: F-Pilus

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Supramolecule #1000: Bacteriophage MS2 bound to its receptor, the E. coli F-pilus

SupramoleculeName: Bacteriophage MS2 bound to its receptor, the E. coli F-pilus
type: sample / ID: 1000 / Details: Sub-tomographic averaging of virus-decorated pili
Oligomeric state: One T=3 icosahedral virus bound to a pilus fibre
Number unique components: 2

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Supramolecule #1: Enterobacterio phage MS2

SupramoleculeName: Enterobacterio phage MS2 / type: virus / ID: 1 / NCBI-ID: 12022 / Sci species name: Enterobacterio phage MS2 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 290 Å / T number (triangulation number): 3

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Supramolecule #2: F-Pilus

SupramoleculeName: F-Pilus / type: organelle_or_cellular_component / ID: 2 / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

GridDetails: 200 mesh lacey carbon grids, glow discharged in air.
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 23000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 23000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
DateJan 1, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k)

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 39.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, PEET / Number subtomograms used: 1000

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Atomic model buiding 1

Initial modelPDB ID:

2ms2


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4bp7:
Asymmetric structure of a virus-receptor complex

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