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- EMDB-6444: Atomic structure of a non-enveloped virus reveals pH sensors for ... -

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Basic information

Entry
Database: EMDB / ID: EMD-6444
TitleAtomic structure of a non-enveloped virus reveals pH sensors for a coordinated process of cell entry
Map dataThe whole map of BTV virion at pH 8.8 without imposing a reverse B-factor to boost high frequency signals
Sample
  • Sample: BTV virion at pH 8.8
  • Virus: Bluetongue virus 1
KeywordsNon-enveloped virus / cell entry / cryo-EM / pH sensor
Biological speciesBluetongue virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang X / Patel A / Celma C / Roy P / Zhou ZH
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Atomic model of a nonenveloped virus reveals pH sensors for a coordinated process of cell entry.
Authors: Xing Zhang / Avnish Patel / Cristina C Celma / Xuekui Yu / Polly Roy / Z Hong Zhou /
Abstract: Viruses sense environmental cues such as pH to engage in membrane interactions for cell entry during infection, but how nonenveloped viruses sense pH is largely undefined. Here, we report both high- ...Viruses sense environmental cues such as pH to engage in membrane interactions for cell entry during infection, but how nonenveloped viruses sense pH is largely undefined. Here, we report both high- and low-pH structures of bluetongue virus (BTV), which enters cells via a two-stage endosomal process. The receptor-binding protein VP2 possesses a zinc finger that may function to maintain VP2 in a metastable state and a conserved His866, which senses early-endosomal pH. The membrane-penetration protein VP5 has three domains: dagger, unfurling and anchoring. Notably, the β-meander motif of the anchoring domain contains a histidine cluster that can sense late-endosomal pH and also possesses four putative membrane-interaction elements. Exposing BTV to low pH detaches VP2 and dramatically refolds the dagger and unfurling domains of VP5. Our biochemical and structure-guided-mutagenesis studies support these coordinated pH-sensing mechanisms.
History
DepositionAug 27, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseDec 9, 2015-
UpdateJan 20, 2016-
Current statusJan 20, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6444.jpg

Downloads & links

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Map

FileDownload / File: emd_6444.map.gz / Format: CCP4 / Size: 3.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe whole map of BTV virion at pH 8.8 without imposing a reverse B-factor to boost high frequency signals
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 1024 pix.
= 1060.864 Å		1.04 Å/pix.
x 1024 pix.
= 1060.864 Å		1.04 Å/pix.
x 1024 pix.
= 1060.864 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.036 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.015 / Movie #1: 0.01
Minimum - Maximum-0.01647704 - 0.03365718
Average (Standard dev.)-0.00110645 (±0.00342248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions102410241024
Spacing102410241024
CellA=B=C: 1060.864 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0361.0361.036
M x/y/z102410241024
origin x/y/z0.0000.0000.000
length x/y/z1060.8641060.8641060.864
α/β/γ90.00090.00090.000
start NX/NY/NZ-8211244
NX/NY/NZ115138149
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS102410241024
D min/max/mean-0.0160.034-0.001

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Supplemental data

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Sample components

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Entire : BTV virion at pH 8.8

EntireName: BTV virion at pH 8.8
Components
  • Sample: BTV virion at pH 8.8
  • Virus: Bluetongue virus 1

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Supramolecule #1000: BTV virion at pH 8.8

SupramoleculeName: BTV virion at pH 8.8 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Bluetongue virus 1

SupramoleculeName: Bluetongue virus 1 / type: virus / ID: 1 / NCBI-ID: 35327 / Sci species name: Bluetongue virus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Capra hircus (goat) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 800 Å / T number (triangulation number): 13

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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: 8.8
GridDetails: 400 mesh grid with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureAverage: 82 K
DateNov 29, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 1630 / Average electron dose: 20 e/Å2 / Bits/pixel: 32
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 24140 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.3 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 14000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: OTHER / Software - Name: Frealign / Number images used: 5008
Final two d classificationNumber classes: 1

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