[English] 日本語
Yorodumi
- EMDB-10505: Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10505
TitleMultiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E symmetry expansion+genome focused classification
Map dataNone
Sample
  • Virus: Bovine enterovirus type 1
    • Protein or peptide: Bovine Enterovirus 1 VP1
    • Protein or peptide: Bovine Enterovirus 1 VP2
    • Protein or peptide: Bovine Enterovirus 1 VP3
    • Protein or peptide: Bovine Enterovirus 1 VP4
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / : / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 ...Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / 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 speciesBovine enterovirus type 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsChandler-Bostock R / Mata CP / Bingham R / Dykeman EC / Meng B / Tuthill TJ / Rowlands DJ / Ranson NA / Twarock R / Stockley PG
Funding support United Kingdom, 7 items
OrganizationGrant numberCountry
Wellcome Trust110145 United Kingdom
Wellcome Trust110146 United Kingdom
Wellcome Trust089311/Z/09/Z United Kingdom
Wellcome Trust090932/Z/09/Z United Kingdom
Wellcome Trust106692 United Kingdom
Royal SocietyLT130088 United Kingdom
Royal SocietyRSWF/R1/180009 United Kingdom
CitationJournal: PLoS Pathog / Year: 2020
Title: Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts.
Authors: Rebecca Chandler-Bostock / Carlos P Mata / Richard J Bingham / Eric C Dykeman / Bo Meng / Tobias J Tuthill / David J Rowlands / Neil A Ranson / Reidun Twarock / Peter G Stockley /
Abstract: Picornaviruses are important viral pathogens, but despite extensive study, the assembly process of their infectious virions is still incompletely understood, preventing the development of anti-viral ...Picornaviruses are important viral pathogens, but despite extensive study, the assembly process of their infectious virions is still incompletely understood, preventing the development of anti-viral strategies targeting this essential part of the life cycle. We report the identification, via RNA SELEX and bioinformatics, of multiple RNA sites across the genome of a typical enterovirus, enterovirus-E (EV-E), that each have affinity for the cognate viral capsid protein (CP) capsomer. Many of these sites are evolutionarily conserved across known EV-E variants, suggesting they play essential functional roles. Cryo-electron microscopy was used to reconstruct the EV-E particle at ~2.2 Å resolution, revealing extensive density for the genomic RNA. Relaxing the imposed symmetry within the reconstructed particles reveals multiple RNA-CP contacts, a first for any picornavirus. Conservative mutagenesis of the individual RNA-contacting amino acid side chains in EV-E, many of which are conserved across the enterovirus family including poliovirus, is lethal but does not interfere with replication or translation. Anti-EV-E and anti-poliovirus aptamers share sequence similarities with sites distributed across the poliovirus genome. These data are consistent with the hypothesis that these RNA-CP contacts are RNA Packaging Signals (PSs) that play vital roles in assembly and suggest that the RNA PSs are evolutionarily conserved between pathogens within the family, augmenting the current protein-only assembly paradigm for this family of viruses.
History
DepositionNov 19, 2019-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateJun 23, 2021-
Current statusJun 23, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0324
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0324
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10505.png

Downloads & links

-
Map

FileDownload / File: emd_10505.map.gz / Format: CCP4 / Size: 391 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 468 pix.
= 498.42 Å		1.07 Å/pix.
x 468 pix.
= 498.42 Å		1.07 Å/pix.
x 468 pix.
= 498.42 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0324 / Movie #1: 0.0324
Minimum - Maximum-0.33268285 - 0.5397816
Average (Standard dev.)0.0016551134 (±0.027893718)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-234-234-234
Dimensions468468468
Spacing468468468
CellA=B=C: 498.42 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z468468468
origin x/y/z0.0000.0000.000
length x/y/z498.420498.420498.420
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-234-234-234
NC/NR/NS468468468
D min/max/mean-0.3330.5400.002

-
Supplemental data

-
Sample components

-
Entire : Bovine enterovirus type 1

EntireName: Bovine enterovirus type 1
Components
  • Virus: Bovine enterovirus type 1
    • Protein or peptide: Bovine Enterovirus 1 VP1
    • Protein or peptide: Bovine Enterovirus 1 VP2
    • Protein or peptide: Bovine Enterovirus 1 VP3
    • Protein or peptide: Bovine Enterovirus 1 VP4

-
Supramolecule #1: Bovine enterovirus type 1

SupramoleculeName: Bovine enterovirus type 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1248331 / Sci species name: Bovine enterovirus type 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / T number (triangulation number): 3

-
Macromolecule #1: Bovine Enterovirus 1 VP1

MacromoleculeName: Bovine Enterovirus 1 VP1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bovine enterovirus type 1
SequenceString: NDPGKMLKDA IDKQVAGALV AGTTTSTHSV ATDSTPALQA A ETGATSTA RDESMIETRT IVPTHGIHET SVESFFGRSS LVGMPLLATG TSITNWRIDF RE FVQLRAK MSWFTYMRFD VEFTIIATSS TGQNVTTEQH TTYQVMYVPP GAPVPSNQDS FQW QSGCNP ...String:
NDPGKMLKDA IDKQVAGALV AGTTTSTHSV ATDSTPALQA A ETGATSTA RDESMIETRT IVPTHGIHET SVESFFGRSS LVGMPLLATG TSITNWRIDF RE FVQLRAK MSWFTYMRFD VEFTIIATSS TGQNVTTEQH TTYQVMYVPP GAPVPSNQDS FQW QSGCNP SVFADTDGPP AQFSVPFMSS ANAYSTVYDG YARFMDTDPD RYGILPSNFL GFMY FRTLE DAAHQVRFRI CAKIKHTSCW IPRAPRQAPY KKRYNLVFSG DSDRICSNRA SLTSY

-
Macromolecule #2: Bovine Enterovirus 1 VP2

MacromoleculeName: Bovine Enterovirus 1 VP2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bovine enterovirus type 1
SequenceString: SPSAEACGYS DRVAQLTLGN STITTQEAAN ICVAYGCWPA KLSDTDATSV D KPTEPGVS ADAFYTLRSK PWQADSKGWY WKLPDALNNT GMFGQNAQFH YIYRGGWAVH VQ CNATKFH QGTLLVLAIP EHQIATQEQP AFDRTMPGSE GGTFQEPFWL EDGTSLGNSL IYP ...String:
SPSAEACGYS DRVAQLTLGN STITTQEAAN ICVAYGCWPA KLSDTDATSV D KPTEPGVS ADAFYTLRSK PWQADSKGWY WKLPDALNNT GMFGQNAQFH YIYRGGWAVH VQ CNATKFH QGTLLVLAIP EHQIATQEQP AFDRTMPGSE GGTFQEPFWL EDGTSLGNSL IYP HQWINL RTNNSATLIL PYVNAIPMDS AIRHSNWTLA IIPVAPLKYA AETTPLVPIT VTIA PMETE YNGLRRAIAS NQ

-
Macromolecule #3: Bovine Enterovirus 1 VP3

MacromoleculeName: Bovine Enterovirus 1 VP3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Bovine enterovirus type 1
SequenceString: GLPTKPGPGS YQFMTTDEDC SPCILPDFQP TLEIFIPGKV NNL LEIAQV ESILEANNRE GVEGVERYVI PVSVQDALDA QIYALRLELG GSGPLSSSLL GTLA KHYTQ WSGSVEITCM FTGTFMTTGK VLLAYTPPGG DMPRNREEAM LGTHVVWDFG LQSSI TLVI ...String:
GLPTKPGPGS YQFMTTDEDC SPCILPDFQP TLEIFIPGKV NNL LEIAQV ESILEANNRE GVEGVERYVI PVSVQDALDA QIYALRLELG GSGPLSSSLL GTLA KHYTQ WSGSVEITCM FTGTFMTTGK VLLAYTPPGG DMPRNREEAM LGTHVVWDFG LQSSI TLVI PWISASHFRG VSNDDVLNYQ YYAAGHVTIW YQTNMVIPPG FPNTAGIIMM IAAQPN FSF RIQKDREDMT QTAILQ

-
Macromolecule #4: Bovine Enterovirus 1 VP4

MacromoleculeName: Bovine Enterovirus 1 VP4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Bovine enterovirus type 1
SequenceString:
GAQLSRNTAG SHTTGTYATG GSTINYNNIN YYSHAASAAQ NKQDFTQDPS KFTQPIADV IKETAVPLK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Component - Formula: PBS / Details: PBS
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 8785 / Average exposure time: 1.0 sec. / Average electron dose: 49.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 260348
CTF correctionSoftware - Name: Gctf
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 835940
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)

+
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