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- EMDB-6445: Atomic structure of a non-enveloped virus reveals pH sensors for ... -

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Basic information

Entry
Database: EMDB / ID: 6445
TitleAtomic structure of a non-enveloped virus reveals pH sensors for a coordinated process of cell entry
KeywordsNon-enveloped virus / cell entry / cryo-EM / pH sensor
SampleBTV virion at pH 3.4 without imposing a reverse B-factor to boost high frequency signals
SourceBluetongue virus 1 / virus
Map dataThe whole map of BTV virion at pH 3.4 without imposing a reverse B-factor to boost high frequency signals
Methodsingle particle (icosahedral) reconstruction, at 3.3 Å resolution
AuthorsZhang X / Patel A / Celma C / Roy P / Zhou ZH
CitationNat. Struct. Mol. Biol., 2016, 23, 74-80

Nat. Struct. Mol. Biol., 2016, 23, 74-80 Yorodumi Papers
Atomic model of a nonenveloped virus reveals pH sensors for a coordinated process of cell entry.
Xing Zhang / Avnish Patel / Cristina C Celma / Xuekui Yu / Polly Roy / Z Hong Zhou

DateDeposition: Aug 27, 2015 / Header (metadata) release: Sep 23, 2015 / Map release: Dec 9, 2015 / Last update: Jan 20, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF CHIMERA
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Map

Fileemd_6445.map.gz (map file in CCP4 format, 524289 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.89 Å/pix.
= 967.68 Å
512 pix
1.89 Å/pix.
= 967.68 Å
512 pix
1.89 Å/pix.
= 967.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.89 Å
Density
Contour Level:0.021 (by emdb), 0.01 (movie #1):
Minimum - Maximum-0.03486086 - 0.07199354
Average (Standard dev.)-0.00617108 (0.02015702)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin000
Limit511511511
Spacing512512512
CellA=B=C: 967.68 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.891.891.89
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z967.680967.680967.680
α/β/γ90.00090.00090.000
start NX/NY/NZ-8211244
NX/NY/NZ115138149
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0350.072-0.006

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Supplemental data

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Sample components

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Entire BTV virion at pH 3.4 without imposing a reverse B-factor to boost...

EntireName: BTV virion at pH 3.4 without imposing a reverse B-factor to boost high frequency signals
Number of components: 1

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Component #1: virus, Bluetongue virus 1

VirusName: Bluetongue virus 1 / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Bluetongue virus 1 / virus
Source (natural)Host Species: Capra hircus / mammal / ヤギ / image: Capra aegagrus
Host category: VERTEBRATES

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: citrate buffer / pH: 3.4
Support filmthin carbon on a lacey holey carbon support film
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: May 11, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 350 / Sampling size: 15 microns / Bit depth: 32

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 4503
3D reconstructionAlgorithm: reference match / Software: Frealign / CTF correction: each particle / Resolution: 3.3 Å / Resolution method: FSC 0.143, semi-independent

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