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- PDB-7kv8: Chimeric flavivirus between Binjari virus and Dengue virus serotype-2 -

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Basic information

Entry
Database: PDB / ID: 7kv8
TitleChimeric flavivirus between Binjari virus and Dengue virus serotype-2
Components
  • Envelope protein E
  • Matrix protein M
KeywordsVIRUS / Flavivirus / glycoprotein / entry / fusion
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / 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 / 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 / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus envelope glycoprotein E, stem/anchor domain / 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 envelope glycoprotein E, stem/anchor domain / 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. / 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 / 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
Chem-1Q0 / Chem-6OU / Core protein / Core protein / Core protein / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 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: 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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Nov 24, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref_seq
Item: _atom_site.auth_seq_id / _database_2.pdbx_DOI ..._atom_site.auth_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_end

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Structure visualization

Movie
  • 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-23042
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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: Matrix protein M
b: Matrix protein M
c: Matrix protein M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,38518
Polymers187,9726
Non-polymers5,41312
Water8,179454
1
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
a: Matrix protein M
b: Matrix protein M
c: Matrix protein M
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)11,603,1101080
Polymers11,278,331360
Non-polymers324,779720
Water6,485360
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: Matrix protein M
b: Matrix protein M
c: Matrix protein M
hetero molecules
x 5


  • icosahedral pentamer
  • 967 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)966,92690
Polymers939,86130
Non-polymers27,06560
Water54030
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
a: Matrix protein M
b: Matrix protein M
c: Matrix protein M
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.16 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,160,311108
Polymers1,127,83336
Non-polymers32,47872
Water64936
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

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Protein , 2 types, 6 molecules ABCabc

#1: Protein Envelope protein E /


Mass: 54272.578 Da / Num. of mol.: 3 / Fragment: UNP residues 281-775
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Strain: ET200 / Cell line (production host): C6/36 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: A0A1X9PLJ6, UniProt: P18356*PLUS
#2: Protein Matrix protein M


Mass: 8384.814 Da / Num. of mol.: 3 / Fragment: UNP residues 206-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Strain: ET300 / Cell line (production host): C6/36 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: A0A7D0JW86, UniProt: A0A346TIJ9*PLUS

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Sugars , 1 types, 6 molecules

#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 460 molecules

#4: Chemical ChemComp-6OU / [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C39H76NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#5: Chemical ChemComp-1Q0 / (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl dihydrogen phosphate


Mass: 643.918 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C36H70NO6P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Binjari virusVIRUSAedes albopictus C6/36 cells#1-#20MULTIPLE SOURCES
2M and E from Dengue virus serotype-2 isolate ET300 form a complex that assembles into anti-parallel dimers, (M-E)2, in the T=3 icosahedral particle.COMPLEXThe prM and E genes of Dengue virus serotype-2 isolate ET300 were integrated into the Binjari virus genome using the Circular Polymerase Extension Reaction#1-#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
1122 MDaNO
2111.2 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Binjari virus2305258BFTA20
22Dengue virus 211060ET200/300
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.: 7.7 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, -2 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: 130000 X / Calibrated defocus min: 300 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12.5 sec. / Electron dose: 67.7 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: 4722
Image scansMovie frames/image: 50 / Used frames/image: 1-50

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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: 196292
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111223 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6CO8

6co8

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