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- EMDB-6239: Atomic structure of a non-enveloped virus reveals pH sensors for ... -

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Basic information

Entry
Database: EMDB / ID: EMD-6239
TitleAtomic structure of a non-enveloped virus reveals pH sensors for a coordinated process of cell entry
Map dataReconstruction of BTV virion
Sample
  • Sample: VP2 of Bluetongue Virus
  • Virus: Bluetongue virus 1
KeywordsNon-enveloped virus / cell entry / cryo-EM / pH sensor
Function / homologyOuter capsid protein VP2, Orbivirus / Orbivirus outer capsid protein VP2 / viral inner capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity / Outer capsid protein VP2
Function and homology information
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
DepositionJan 9, 2015-
Header (metadata) releaseJan 21, 2015-
Map releaseDec 9, 2015-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j9d
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6239.gif

Downloads & links

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Map

FileDownload / File: emd_6239.map.gz / Format: CCP4 / Size: 11.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of BTV virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.01 Å/pix.
x 146 pix.
= 147.46 Å		1.01 Å/pix.
x 132 pix.
= 133.32 Å		1.01 Å/pix.
x 160 pix.
= 161.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-3.04202008 - 5.23893023
Average (Standard dev.)0.01341875 (±0.21973737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-1345290
Dimensions132160146
Spacing160132146
CellA: 133.31999 Å / B: 161.6 Å / C: 147.45999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.011.011.01
M x/y/z132160146
origin x/y/z0.0000.0000.000
length x/y/z133.320161.600147.460
α/β/γ90.00090.00090.000
start NX/NY/NZ-1345290
NX/NY/NZ132160146
MAP C/R/S213
start NC/NR/NS5-134290
NC/NR/NS160132146
D min/max/mean-3.0425.2390.013

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Supplemental data

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Supplemental map: emd 6239 additional 1.map

Fileemd_6239_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : VP2 of Bluetongue Virus

EntireName: VP2 of Bluetongue Virus
Components
  • Sample: VP2 of Bluetongue Virus
  • Virus: Bluetongue virus 1

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Supramolecule #1000: VP2 of Bluetongue Virus

SupramoleculeName: VP2 of Bluetongue Virus / 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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