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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 dataNon-Structural protein 1 of bluetongue virus, primary map
Sample
  • Complex: Non-structural protein 1 (tubule)
    • Protein or peptide: Non-structural protein 1
KeywordsBluetongue Virus Non-structural protein 1 / VIRAL PROTEIN
Function / homologyOrbivirus non-structural protein NS1/hydrophobic tubular protein / Orbivirus non-structural protein NS1, or hydrophobic tubular protein / Non-structural protein NS1
Function and homology information
Biological speciesBluetongue virus (serotype 1 / isolate South Africa) / Bluetongue virus 23
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsKerviel A / Ge 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
Wellcome Trust100218 United Kingdom
National Science Foundation (NSF, United States)MCB140140 United States
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.
History
DepositionDec 4, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseMar 13, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing 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

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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)
AnnotationNon-Structural protein 1 of bluetongue virus, primary map
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)
Components
  • Complex: Non-structural protein 1 (tubule)
    • Protein or peptide: Non-structural protein 1

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Supramolecule #1: Non-structural protein 1 (tubule)

SupramoleculeName: Non-structural protein 1 (tubule) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bluetongue virus (serotype 1 / isolate South Africa)

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Macromolecule #1: Non-structural protein 1

MacromoleculeName: Non-structural protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bluetongue virus 23
Molecular weightTheoretical: 64.554984 KDa
SequenceString: MERFLRKYNI SGDYANATRT FLAISPQWTC SHLKRNCLFN GMCAKQNFER AMIAATDAEE PAKAYRLVEL AKEAMYDRET VWLQCFKSF SQPYEEDIEG KMKRCGAQLL EDYRKNGMMD EAVKQSALVN SERVRLDDSL SAMPYIYVPI KEGQIVNPTF I SRYRQIAY ...String:
MERFLRKYNI SGDYANATRT FLAISPQWTC SHLKRNCLFN GMCAKQNFER AMIAATDAEE PAKAYRLVEL AKEAMYDRET VWLQCFKSF SQPYEEDIEG KMKRCGAQLL EDYRKNGMMD EAVKQSALVN SERVRLDDSL SAMPYIYVPI KEGQIVNPTF I SRYRQIAY YFYSPNLADD WIDPNLFGIR GQHNQIKREI ERQVNTCPYT GYKGRVLQVM FLPIQLINFL RMDDFAKHFN RY ASMAIQQ YLRVGYAEEV RYVQQLFGKI PTGEFPLHHM MLMRRDFPTR DRSIVEARVR RSGDENWQSW LLPMIIVREG LDH QDRWEW LIDYMDRKHT CQLCYLKHSK QIPTCGVIDV RASELTGCSP FKTVKIEEHV GNNSVFETKL VRDEQIGRIG DHYY TTNCY TGAEALITTA IHIHRWIRGC GIWNDEGWRE GIFMLGRVLL RWELTKAQRS ALLRLFCFVC YGYAPRADGT IPDWN NLGS FLDTILKGPE LSEDEDERAY ATMFEMVRCI ITLCYAEKVH FAGFAAPACE SGEVINLAAR MSQMRMEY

UniProtKB: Non-structural protein NS1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chlorideSalt
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.0 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specialist opticsEnergy filter - Name: GIF Quantum LS
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 3-19 / Number grids imaged: 2 / Number real images: 5006 / Average exposure time: 10.0 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Helical parameters - Δz: 8.83 Å
Applied symmetry - Helical parameters - Δ&Phi: -17.50 °
Applied symmetry - Helical parameters - Axial symmetry: D2 (2x2 fold dihedral)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: OTHER / Software - Name: RELION (ver. 2.0) / Number images used: 7800

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6n9y:
Atomic structure of Non-Structural protein 1 of bluetongue virus

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