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

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Entry
Database: PDB / ID: 6n9y
TitleAtomic structure of Non-Structural protein 1 of bluetongue virus
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / Bluetongue Virus Non-structural protein 1
Function / homologyOrbivirus non-structural protein NS1/hydrophobic tubular protein / Orbivirus non-structural protein NS1, or hydrophobic tubular protein / NS1
Function and homology information
Specimen sourceBluetongue virus 23
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 4 Å resolution
AuthorsKerviel, A. / Ge, P. / Lai, M. / Jih, J. / Boyce, M. / Zhang, X. / Zhou, Z.H. / Roy, P.
Funding supportUnited States , United Kingdom , 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI094386United States
Wellcome Trust100218United Kingdom
National Science Foundation (United States)MCB140140United 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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 4, 2018 / Release: Mar 13, 2019

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Assembly

Deposited unit
A: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)64,5551
Polyers64,5551
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)29620

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Components

#1: Protein/peptide Non-structural protein 1


Mass: 64554.984 Da / Num. of mol.: 1 / Source: (natural) Bluetongue virus 23 / References: UniProt: L7WU69

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Non-structural protein 1 (tubule) / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bluetongue virus (serotype 1 / isolate South Africa)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer ID
120 mMTrisC4H11NO31
2150 mMSaltNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated defocus min: 1200 nm / Calibrated defocus max: 4000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 2 / Number of real images: 5006
EM imaging opticsEnergyfilter name: GIF Quantum LS
Image scansMovie frames/image: 50 / Used frames/image: 3-19

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN1.8particle selection
2Leginonimage acquisition
4CTFFIND3CTF correction
10RELION2.0final Euler assignment
11RELION1.4classificationIHRSR extension
12RELION2.03D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -17.5 deg. / Axial rise/subunit: 8.83 Å / Axial symmetry: D2
3D reconstructionResolution: 4 Å / Resolution method: OTHER / Number of particles: 7800 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL

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