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- EMDB-23043: Chimeric flavivirus between Binjari virus and West Nile (Kunjin) virus -

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Basic information

Entry
Database: EMDB / ID: EMD-23043
TitleChimeric flavivirus between Binjari virus and West Nile (Kunjin) virus
Map dataLocal resolution filtered map
Sample
  • Virus: Binjari virus
    • Complex: M and E from West Nile virus isolate NSW2011 form a complex that assembles into anti-parallel dimers, (M-E)2, in the T=3 icosahedral particle.
      • Protein or peptide: envelope protein E
      • Protein or peptide: Matrix protein M
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont entry into host cell / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesKunjin virus / Binjari virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsHardy JM / Venugopal HV / Newton ND / Watterson D / Coulibaly FJ
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1164216 Australia
CitationJournal: Nat Commun / Year: 2021
Title: A unified route for flavivirus structures uncovers essential pocket factors conserved across pathogenic viruses.
Authors: Joshua M Hardy / Natalee D Newton / Naphak Modhiran / Connor A P Scott / Hariprasad Venugopal / Laura J Vet / Paul R Young / Roy A Hall / Jody Hobson-Peters / Fasséli Coulibaly / Daniel Watterson /
Abstract: The epidemic emergence of relatively rare and geographically isolated flaviviruses adds to the ongoing disease burden of viruses such as dengue. Structural analysis is key to understand and combat ...The epidemic emergence of relatively rare and geographically isolated flaviviruses adds to the ongoing disease burden of viruses such as dengue. Structural analysis is key to understand and combat these pathogens. Here, we present a chimeric platform based on an insect-specific flavivirus for the safe and rapid structural analysis of pathogenic viruses. We use this approach to resolve the architecture of two neurotropic viruses and a structure of dengue virus at 2.5  Å, the highest resolution for an enveloped virion. These reconstructions allow improved modelling of the stem region of the envelope protein, revealing two lipid-like ligands within highly conserved pockets. We show that these sites are essential for viral growth and important for viral maturation. These findings define a hallmark of flavivirus virions and a potential target for broad-spectrum antivirals and vaccine design. We anticipate the chimeric platform to be widely applicable for investigating flavivirus biology.
History
DepositionNov 27, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.048
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.048
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kv9
  • Surface level: 0.048
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kv9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23043.png

Downloads & links

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Map

FileDownload / File: emd_23043.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered map
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.048 / Movie #1: 0.048
Minimum - Maximum-0.23312086 - 0.4469227
Average (Standard dev.)0.0007606822 (±0.019488212)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 603.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z603.000603.000603.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.2330.4470.001

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Supplemental data

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Mask #1

Fileemd_23043_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unmasked sharpened map

Fileemd_23043_additional_1.map
AnnotationUnmasked sharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Masked sharpened map

Fileemd_23043_additional_2.map
AnnotationMasked sharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unmasked unsharpened map

Fileemd_23043_additional_3.map
AnnotationUnmasked unsharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_23043_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_23043_half_map_2.map
AnnotationHalf map 2
Projections & Slices
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Sample components

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Entire : Binjari virus

EntireName: Binjari virus
Components
  • Virus: Binjari virus
    • Complex: M and E from West Nile virus isolate NSW2011 form a complex that assembles into anti-parallel dimers, (M-E)2, in the T=3 icosahedral particle.
      • Protein or peptide: envelope protein E
      • Protein or peptide: Matrix protein M
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Binjari virus

SupramoleculeName: Binjari virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Aedes albopictus C6/36 cells / NCBI-ID: 2305258 / Sci species name: Binjari virus / Sci species strain: BFTA20 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Ochlerotatus normanensis (mosquito)
Molecular weightTheoretical: 11.2 MDa
Virus shellShell ID: 1 / Diameter: 470.0 Å / T number (triangulation number): 3

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Supramolecule #2: M and E from West Nile virus isolate NSW2011 form a complex that ...

SupramoleculeName: M and E from West Nile virus isolate NSW2011 form a complex that assembles into anti-parallel dimers, (M-E)2, in the T=3 icosahedral particle.
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: The prM and E genes of West Nile virus isolate NSW2011 were integrated into the Binjari virus genome using the Circular Polymerase Extension Reaction
Source (natural)Organism: Kunjin virus
Recombinant expressionOrganism: Aedes albopictus (Asian tiger mosquito) / Recombinant cell: C6/36

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Macromolecule #1: envelope protein E

MacromoleculeName: envelope protein E / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Kunjin virus
Molecular weightTheoretical: 53.787098 KDa
Recombinant expressionOrganism: Aedes albopictus (Asian tiger mosquito)
SequenceString: FNCLGMSNRD FLEGVSGATW VDLVLEGDSC VTIMSKDKPT IDVRMMNMEA ANLAEVRSYC YLATVSELST KAACPTMGEA HNDKRADPS FVCKQGVVDR GWGNGCGLFG KGSIDTCAKF ACSTKATGRT ILKENIKYEV AIFVHGPTTV ESHGNYSTQT G AAQAGRFS ...String:
FNCLGMSNRD FLEGVSGATW VDLVLEGDSC VTIMSKDKPT IDVRMMNMEA ANLAEVRSYC YLATVSELST KAACPTMGEA HNDKRADPS FVCKQGVVDR GWGNGCGLFG KGSIDTCAKF ACSTKATGRT ILKENIKYEV AIFVHGPTTV ESHGNYSTQT G AAQAGRFS ITPAAPSYTL KLGEYGEVTV DCEPRSGIDT SAYYVMTVGT KTFLVHREWF MDLNLPWSSA ESNVWRNRET LM EFEEPHA TKQSVIALGS QEGALHQALA GAIPVEFSSN TVKLTSGHLK CRVKMEKLQL KGTTYGVCSK AFRFLGTPAD TGH GTVVLE LQYTGTDGPC KIPISSVASL NDLTPVGRLV TVNPFVSVST ANAKVLIELE PPFGDSYIVV GRGEQQINHH WHKS GSSIG KAFTATLKGA QRLAALGDTA WDFGSVGGVF TSVGKAVHQV FGGAFRSLFG GMSWITQGLL GALLLWMGIN ARDRS IAFT FLAVGGVLLF LSVNVHA

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Macromolecule #2: Matrix protein M

MacromoleculeName: Matrix protein M / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Kunjin virus
Molecular weightTheoretical: 8.251602 KDa
Recombinant expressionOrganism: Aedes albopictus (Asian tiger mosquito)
SequenceString:
SLTVQTHGES TLSNKKGAWM DSTKATRYLV KTESWILRNP GYALVAAVIG WMLGSNTMQR VVFTVLLLLV APAYS

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration4 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
12.0 mM(HOCH2)3CNH2Tris
120.0 mMNaClSodium chloridesodium chloride
1.0 mMC10H16N2O8Ethylenediaminetetraacetic acid (EDTA)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 0 second wait time 2 second blot time -12 blot force 1 second drain time.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 1.7 µm / Calibrated defocus min: 0.3 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
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: SUPER-RESOLUTION / Digitization - Frames/image: 1-17 / Number grids imaged: 1 / Number real images: 3209 / Average exposure time: 12.8 sec. / Average electron dose: 57.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 130675
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP
EMDB ID:

5296

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 16133 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 40058
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6co8

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7kv9:
Chimeric flavivirus between Binjari virus and West Nile (Kunjin) virus

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