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- EMDB-23330: Binjari virus (BinJV) complexed with pr-specific Fab 2A7 -

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Basic information

Entry
Database: EMDB / ID: EMD-23330
TitleBinjari virus (BinJV) complexed with pr-specific Fab 2A7
Map dataResolution filtered map
Sample
  • Complex: Binjari virus complexed with pr-specific Fab 2A7
    • Complex: 2A7 Fab
    • Virus: Binjari virus
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / 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, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / 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 conserved C-terminal 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. / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse) / Binjari virus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.6 Å
AuthorsCoulibaly FJ / Newton ND / Hardy JM / Watterson D
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1164216 Australia
CitationJournal: Sci Adv / Year: 2021
Title: The structure of an infectious immature flavivirus redefines viral architecture and maturation.
Authors: Natalee D Newton / Joshua M Hardy / Naphak Modhiran / Leon E Hugo / Alberto A Amarilla / Summa Bibby / Hariprasad Venugopal / Jessica J Harrison / Renee J Traves / Roy A Hall / Jody Hobson- ...Authors: Natalee D Newton / Joshua M Hardy / Naphak Modhiran / Leon E Hugo / Alberto A Amarilla / Summa Bibby / Hariprasad Venugopal / Jessica J Harrison / Renee J Traves / Roy A Hall / Jody Hobson-Peters / Fasséli Coulibaly / Daniel Watterson /
Abstract: Flaviviruses are the cause of severe human diseases transmitted by mosquitoes and ticks. These viruses use a potent fusion machinery to enter target cells that needs to be restrained during viral ...Flaviviruses are the cause of severe human diseases transmitted by mosquitoes and ticks. These viruses use a potent fusion machinery to enter target cells that needs to be restrained during viral assembly and egress. A molecular chaperone, premembrane (prM) maintains the virus particles in an immature, fusion-incompetent state until they exit the cell. Taking advantage of an insect virus that produces particles that are both immature and infectious, we determined the structure of the first immature flavivirus with a complete spike by cryo-electron microscopy. Unexpectedly, the prM chaperone forms a supporting pillar that maintains the immature spike in an asymmetric and upright state, primed for large rearrangements upon acidification. The collapse of the spike along a path defined by the prM chaperone is required, and its inhibition by a multivalent immunoglobulin M blocks infection. The revised architecture and collapse model are likely to be conserved across flaviviruses.
History
DepositionJan 21, 2021-
Header (metadata) releaseMay 26, 2021-
Map releaseMay 26, 2021-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0109165
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0109165
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23330.png

Downloads & links

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Map

FileDownload / File: emd_23330.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationResolution filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.03 Å/pix.
x 432 pix.
= 875.664 Å		2.03 Å/pix.
x 432 pix.
= 875.664 Å		2.03 Å/pix.
x 432 pix.
= 875.664 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.027 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0109165 / Movie #1: 0.0109165
Minimum - Maximum-0.016468005 - 0.03579478
Average (Standard dev.)0.0007135222 (±0.003427503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 875.664 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.0272.0272.027
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z875.664875.664875.664
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0160.0360.001

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Supplemental data

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Mask #1

Fileemd_23330_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_23330_additional_1.map
AnnotationUnmasked sharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Masked sharpened map

Fileemd_23330_additional_2.map
AnnotationMasked sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unmasked unsharpened map

Fileemd_23330_additional_3.map
AnnotationUnmasked unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_23330_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_23330_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Binjari virus complexed with pr-specific Fab 2A7

EntireName: Binjari virus complexed with pr-specific Fab 2A7
Components
  • Complex: Binjari virus complexed with pr-specific Fab 2A7
    • Complex: 2A7 Fab
    • Virus: Binjari virus

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Supramolecule #1: Binjari virus complexed with pr-specific Fab 2A7

SupramoleculeName: Binjari virus complexed with pr-specific Fab 2A7 / type: complex / ID: 1 / Parent: 0
Details: M and E from Binjari virus form a complex that assembles into an asymmetric trimeric spike of prM-E heterodimers. The organization of the immature BinJV particles is T=1 with an asymmetric ...Details: M and E from Binjari virus form a complex that assembles into an asymmetric trimeric spike of prM-E heterodimers. The organization of the immature BinJV particles is T=1 with an asymmetric spike as the basic building block. The 2A7 Fab recognises an epitope on the pr region of BinJV prM and binds the virus with full ocupancy (1:1)
Molecular weightTheoretical: 22 MDa

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Supramolecule #3: 2A7 Fab

SupramoleculeName: 2A7 Fab / type: complex / ID: 3 / Parent: 1
Details: 2A7 Fab fragment generated by cleavage of recombinantly produced IgG 2A7 antibody
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster) / Recombinant cell: CHO
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: Binjari virus

SupramoleculeName: Binjari virus / type: virus / ID: 2 / Parent: 1
Details: M and E from Binjari virus form a complex that assembles into an asymmetric trimeric spike of prM-E heterodimers. The organization of the immature BinJV particles is T=1 with an asymmetric ...Details: M and E from Binjari virus form a complex that assembles into an asymmetric trimeric spike of prM-E heterodimers. The organization of the immature BinJV particles is T=1 with an asymmetric spike as the basic building block.
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: 22 MDa

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mM(HOCH2)3CNH2Tris
120.0 mMNaClsodium chloride
1.0 mMC10H16N2O8EDTA
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK II
DetailsPurified BinJV was complexed with 2A7-Fab at a molar ration of 2:1 Fab:E protein and incubated at 4 C for 2 h.

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 54 / Average exposure time: 5.0 sec. / Average electron dose: 21.95 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1527
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: EMDB MAP
EMDB ID:

20439

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 821
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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