[English] 日本語
Yorodumi
- EMDB-23147: Binjari virus (BinJV) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23147
TitleBinjari virus (BinJV)
Map dataLocal-resolution filtered map
Sample
  • Virus: Binjari virus
    • Protein or peptide: Envelope protein E
    • Protein or peptide: prM protein
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
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 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: 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, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7l30
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7l30
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23147.png

Downloads & links

-
Map

FileDownload / File: emd_23147.map.gz / Format: CCP4 / Size: 512 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: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.06158375 - 0.1203755
Average (Standard dev.)0.0007684218 (±0.0075564524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 686.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z686.080686.080686.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0620.1200.001

-
Supplemental data

-
Sample components

-
Entire : Binjari virus

EntireName: Binjari virus
Components
  • Virus: Binjari virus
    • Protein or peptide: Envelope protein E
    • Protein or peptide: prM protein

-
Supramolecule #1: Binjari virus

SupramoleculeName: Binjari virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
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.
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
Virus shellShell ID: 1 / Diameter: 470.0 Å / T number (triangulation number): 3

-
Macromolecule #1: Envelope protein E

MacromoleculeName: Envelope protein E / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Binjari virus
Molecular weightTheoretical: 53.495086 KDa
Recombinant expressionOrganism: Aedes albopictus (Asian tiger mosquito)
SequenceString: NQCLDVQSRD FVQGVSGGTW VDVVLDHDNC ITIVADGKPS FDIRLSKMSM SKFAEYKRYC LQATMSDVTS IVACPGAGDA HNDKSKNHE YICKAVNNDR GWGNGCVLFG KGSMETCGKF ECKKKMAGKL VARENVESVV TVHVHGASAT DTKGVDTAST A KATITPKA ...String:
NQCLDVQSRD FVQGVSGGTW VDVVLDHDNC ITIVADGKPS FDIRLSKMSM SKFAEYKRYC LQATMSDVTS IVACPGAGDA HNDKSKNHE YICKAVNNDR GWGNGCVLFG KGSMETCGKF ECKKKMAGKL VARENVESVV TVHVHGASAT DTKGVDTAST A KATITPKA SVATLNLNDF GSLEVDCSTD VGMDFGEIVV ADMSGKWWIV NKDWFNELAL PWSTASTTAE VWQARDRLVE FG WPHAAKQ NIYDIGDQEG AVTAAIAQAP MAKWESDKVE LISGILKCKV KLGNLKLRGV TYSMCAQTFT TETRPADTGH GTV AFKVKY VGTDVPCRVP LHIIDSDGGV AAGRVITAHP FVMKQNDYII LEVEPPFGDS KIEIGTGTTK LVEAWHRKGS SIGN AFTAT YKGITKLTVL GEHAWDFNSL GGFGASLGKA VHTLFGGVFR VMFGGMGWLT KIFVGAVLVW LGLGAHDKTI ATTMI LVGS ILMYMAVTVG ALS

-
Macromolecule #2: prM protein

MacromoleculeName: prM protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Binjari virus
Molecular weightTheoretical: 18.946809 KDa
Recombinant expressionOrganism: Aedes albopictus (Asian tiger mosquito)
SequenceString:
ATLRTVGDLT WLNVSTTDVG KWIRVENRHG KGECFVTATD VGTWCSDSVG YECPQIAPAY DPEDLDCYCR NTSTYVTYGR CKNGRSGRS RSKRAITIAP HGEAGLRVGS TKHWTSRATP QRYLMRVEKW VLRHPLPALV LVVLGWMMGR SHGQRAMYIV L MLLVAPSY G

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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 2.5 second blot time -4 blot force 1 second drain time.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.3 µm / Calibrated defocus min: 0.1 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 / Number grids imaged: 1 / Number real images: 6226 / Average exposure time: 12.8 sec. / Average electron dose: 43.2768 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 55992
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP
EMDB ID:

2141

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 26038

-
Atomic model buiding 1

Initial model(PDB ID:

6co8

,

4b03

,

5o6v

)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7l30:
Binjari virus (BinJV)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more