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- EMDB-0383: Atomic structure of Non-Structural protein 1 of bluetongue virus -

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Basic information

Entry
Database: EMDB / ID: EMD-0383
TitleAtomic structure of Non-Structural protein 1 of bluetongue virus
Map data
SampleNon-structural protein 1 (tubule):
Non-structural protein 1
Function / homologyOrbivirus non-structural protein NS1/hydrophobic tubular protein / NS1
Function and homology information
Biological speciesBluetongue virus (serotype 1 / isolate South Africa) / Bluetongue virus 23
Methodhelical reconstruction / cryo EM / Resolution: 4 Å
AuthorsKerviel A / Ge P / Lai M / Jih J / Boyce M / Zhang X / Zhou ZH / Roy P
Funding support United States, United Kingdom, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Science Foundation (NSF, United States)MCB140140 United States
Wellcome Trust100218 United Kingdom
CitationJournal: Nat Microbiol / Year: 2019
Title: Atomic structure of the translation regulatory protein NS1 of bluetongue virus.
Authors: Adeline Kerviel / Peng Ge / Mason Lai / Jonathan Jih / Mark Boyce / Xing Zhang / Z Hong Zhou / Polly Roy /
Abstract: Bluetongue virus (BTV) non-structural protein 1 (NS1) regulates viral protein synthesis and exists as tubular and non-tubular forms in infected cells, but how tubules assemble and how protein ...Bluetongue virus (BTV) non-structural protein 1 (NS1) regulates viral protein synthesis and exists as tubular and non-tubular forms in infected cells, but how tubules assemble and how protein synthesis is regulated are unknown. Here, we report near-atomic resolution structures of two NS1 tubular forms determined by cryo-electron microscopy. The two tubular forms are different helical assemblies of the same NS1 monomer, consisting of an amino-terminal foot, a head and body domains connected to an extended carboxy-terminal arm, which wraps atop the head domain of another NS1 subunit through hydrophobic interactions. Deletion of the C terminus prevents tubule formation but not viral replication, suggesting an active non-tubular form. Two zinc-finger-like motifs are present in each NS1 monomer, and tubules are disrupted by divalent cation chelation and restored by cation addition, including Zn, suggesting a regulatory role of divalent cations in tubule formation. In vitro luciferase assays show that the NS1 non-tubular form upregulates BTV mRNA translation, whereas zinc-finger disruption decreases viral mRNA translation, tubule formation and virus replication, confirming a functional role for the zinc-fingers. Thus, the non-tubular form of NS1 is sufficient for viral protein synthesis and infectious virus replication, and the regulatory mechanism involved operates through divalent cation-dependent conversion between the non-tubular and tubular forms.
Validation ReportPDB-ID: 6n9y

SummaryFull reportAbout validation report
History
DepositionDec 4, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseMar 13, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0314
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0314
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6n9y
  • Surface level: 0.0314
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6n9y
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0383.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214. Å
1.07 Å/pix.
x 200 pix.
= 214. Å
1.07 Å/pix.
x 200 pix.
= 214. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.0314 / Movie #1: 0.0314
Minimum - Maximum-0.043510284 - 0.08262083
Average (Standard dev.)-0.0002076419 (±0.008804378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 214.00002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z214.000214.000214.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.0440.083-0.000

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Supplemental data

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Sample components

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Entire Non-structural protein 1 (tubule)

EntireName: Non-structural protein 1 (tubule) / Number of components: 2

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Component #1: protein, Non-structural protein 1 (tubule)

ProteinName: Non-structural protein 1 (tubule) / Recombinant expression: No
SourceSpecies: Bluetongue virus (serotype 1 / isolate South Africa)

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Component #2: protein, Non-structural protein 1

ProteinName: Non-structural protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 64.554984 kDa
SourceSpecies: Bluetongue virus 23

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: D2 (2x2 fold dihedral) / Delta z: 8.83 Å / Delta phi: -17.5 %deg;
Sample solutionpH: 7.5
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5006

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 4 Å / Resolution method: OTHER

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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