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- PDB-7l30: Binjari virus (BinJV) -

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Basic information

Entry
Database: PDB / ID: 7l30
TitleBinjari virus (BinJV)
Components
  • Envelope protein E
  • prM protein
KeywordsVIRUS / Flavivirus / glycoprotein / fusion
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / extracellular region / ATP binding / metal ion binding
Similarity search - Function
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 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. / 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 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesBinjari virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsHardy, J.M. / Venugopal, H.V. / Newton, N.D. / Watterson, D. / Coulibaly, F.J.
Funding support Australia, 1items
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
DepositionDec 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-23147
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  • EMDB-23147
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
a: prM protein
b: prM protein
c: prM protein


Theoretical massNumber of molelcules
Total (without water)217,3266
Polymers217,3266
Non-polymers00
Water0
1
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
a: prM protein
b: prM protein
c: prM protein
x 60


Theoretical massNumber of molelcules
Total (without water)13,039,541360
Polymers13,039,541360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
a: prM protein
b: prM protein
c: prM protein
x 5


  • icosahedral pentamer
  • 1.09 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,086,62830
Polymers1,086,62830
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
a: prM protein
b: prM protein
c: prM protein
x 6


  • icosahedral 23 hexamer
  • 1.3 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,303,95436
Polymers1,303,95436
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Envelope protein E /


Mass: 53495.086 Da / Num. of mol.: 3 / Fragment: UNP residues 294-790
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Binjari virus / Cell line (production host): C6/36 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: A0A5K6VMX2
#2: Protein prM protein


Mass: 18946.809 Da / Num. of mol.: 3 / Fragment: UNP residues 125-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Binjari virus / Cell line (production host): C6/36 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: A0A5K6VMX2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Binjari virus / Type: VIRUS
Details: M and E from Binjari virus form a complex that assembles into anti-parallel dimers, (M-E)2, in the T=3 icosahedral particle.
Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 22 MDa / Experimental value: NO
Source (natural)Organism: Binjari virus / Strain: BFTA20
Source (recombinant)Organism: Aedes albopictus (Asian tiger mosquito) / Cell: C6/36
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Ochlerotatus normanensis
Virus shellDiameter: 470 nm / Triangulation number (T number): 3
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
112 mMTris(HOCH2)3CNH21
2120 mMsodium chlorideNaClSodium chloride1
31 mMEthylenediaminetetraacetic acid (EDTA)C10H16N2O81
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 0 second wait time 2.5 second blot time -4 blot force 1 second drain time

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 105000 X / Calibrated defocus min: 100 nm / Calibrated defocus max: 4300 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12.8 sec. / Electron dose: 43.2768 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6226
Image scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategory
4Gctf1.06CTF correction
7Coot0.9model fitting
9PHENIX1.18model refinement
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 55992
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26038 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-ID
16CO8

6co8

1
24B03

4b03

1
35O6V

5o6v

1
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 82.99 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006613645
ELECTRON MICROSCOPYf_angle_d0.798618636
ELECTRON MICROSCOPYf_chiral_restr0.04432151
ELECTRON MICROSCOPYf_plane_restr0.00432399
ELECTRON MICROSCOPYf_dihedral_angle_d16.07644361

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