[English] 日本語
Yorodumi
- EMDB-13022: CryoEM structure of human enterovirus 70 native virion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13022
TitleCryoEM structure of human enterovirus 70 native virion
Map dataNative EV70 virion
SampleEnterovirus D70 != Human enterovirus 70 (strain J670/71)

Enterovirus D70

  • Virus: Human enterovirus 70 (strain J670/71)
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
  • Ligand: water
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
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) / Picornavirales 3C/3C-like protease domain ...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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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 speciesEV70, EV-70 / Human enterovirus 70 (strain J670/71)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsFuzik T / Plevka P / Moravcova J
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGX19-25982X Czech Republic
CitationJournal: J Virol / Year: 2022
Title: Structure of Human Enterovirus 70 and Its Inhibition by Capsid-Binding Compounds.
Authors: Tibor Füzik / Jana Moravcová / Sergei Kalynych / Pavel Plevka /
Abstract: Enterovirus 70 (EV70) is a human pathogen belonging to the family . EV70 is transmitted by eye secretions and causes acute hemorrhagic conjunctivitis, a serious eye disease. Despite the severity of ...Enterovirus 70 (EV70) is a human pathogen belonging to the family . EV70 is transmitted by eye secretions and causes acute hemorrhagic conjunctivitis, a serious eye disease. Despite the severity of the disease caused by EV70, its structure is unknown. Here, we present the structures of the EV70 virion, altered particle, and empty capsid determined by cryo-electron microscopy. The capsid of EV70 is composed of the subunits VP1, VP2, VP3, and VP4. The partially collapsed hydrophobic pocket located in VP1 of the EV70 virion is not occupied by a pocket factor, which is commonly present in other enteroviruses. Nevertheless, we show that the pocket can be targeted by the antiviral compounds WIN51711 and pleconaril, which block virus infection. The inhibitors prevent genome release by stabilizing EV70 particles. Knowledge of the structures of complexes of EV70 with inhibitors will enable the development of capsid-binding therapeutics against this virus. Globally distributed enterovirus 70 (EV70) causes local outbreaks of acute hemorrhagic conjunctivitis. The discharge from infected eyes enables the high-efficiency transmission of EV70 in overcrowded areas with low hygienic standards. Currently, only symptomatic treatments are available. We determined the structures of EV70 in its native form, the genome release intermediate, and the empty capsid resulting from genome release. Furthermore, we elucidated the structures of EV70 in complex with two inhibitors that block virus infection, and we describe the mechanism of their binding to the virus capsid. These results enable the development of therapeutics against EV70.
History
DepositionJun 2, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateSep 28, 2022-
Current statusSep 28, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13022.png

Downloads & links

-
Map

FileDownload / File: emd_13022.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNative EV70 virion
Voxel sizeX=Y=Z: 1.063 Å
Density
Contour LevelBy AUTHOR: 1.36
Minimum - Maximum-8.676125 - 12.412011
Average (Standard dev.)-6.499795e-09 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 340.15997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_13022_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_13022_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Enterovirus D70

EntireName: Enterovirus D70
Components
  • Virus: Human enterovirus 70 (strain J670/71)
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP4
  • Ligand: water

-
Supramolecule #1: Human enterovirus 70 (strain J670/71)

SupramoleculeName: Human enterovirus 70 (strain J670/71) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: isolated from infected hTERT RPE1 cells / NCBI-ID: 31915 / Sci species name: Human enterovirus 70 (strain J670/71) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Molecular weightTheoretical: 5.7 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 330.0 Å / T number (triangulation number): 1

-
Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: EV70, EV-70 / Strain: J670/71
Molecular weightTheoretical: 34.049793 KDa
SequenceString: AATTQIGEIV KTVANTVESE IKAELGVIPS LNAVETGATS NTEPEEAIQT RTVINMHGTA ECLVENFLGR SALVCMRSFE YKNHSTSTS SIQKNFFIWT LNTRELVQIR RKMELFTYLR FDTEITIVPT LRLFSSSNVS FSGLPNLTLQ AMYVPTGARK P SSQDSFEW ...String:
AATTQIGEIV KTVANTVESE IKAELGVIPS LNAVETGATS NTEPEEAIQT RTVINMHGTA ECLVENFLGR SALVCMRSFE YKNHSTSTS SIQKNFFIWT LNTRELVQIR RKMELFTYLR FDTEITIVPT LRLFSSSNVS FSGLPNLTLQ AMYVPTGARK P SSQDSFEW QSACNPSVFF KINDPPARLT IPFMSINSAY ANFYDGFAGF EKKATVLYGI NPANTMGNLC LRVVNSYQPV QY TLTVRVY MKPKHIKAWA PRAPRTMPYT NILNNNYAGR SAAPNAPTAI VSHRSTIKTM PNDINLTTA

-
Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: EV70, EV-70 / Strain: J670/71
Molecular weightTheoretical: 27.536107 KDa
SequenceString: SPSAEACGYS DRVLQLKLGN SSIVTQEAAN ICCAYGEWPT YLPDNEAVAI DKPTQPETST DRFYTLKSKK WESNSTGWWW KLPDALNQI GMFGQNVQYH YLYRSGFLCH VQCNATKFHQ GTLLIVAIPE HQIGKKGTGT SASFAEVMKG AEGGVFEQPY L LDDGTSLA ...String:
SPSAEACGYS DRVLQLKLGN SSIVTQEAAN ICCAYGEWPT YLPDNEAVAI DKPTQPETST DRFYTLKSKK WESNSTGWWW KLPDALNQI GMFGQNVQYH YLYRSGFLCH VQCNATKFHQ GTLLIVAIPE HQIGKKGTGT SASFAEVMKG AEGGVFEQPY L LDDGTSLA CALVYPHQWI NLRTNNSATI VLPWMNSAPM DFALRHNNWT LAVIPVCPLA GGTGNTNTYV PITISIAPMC AE YNGLRNA ITQ

-
Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: EV70, EV-70 / Strain: J670/71
Molecular weightTheoretical: 26.717535 KDa
SequenceString: GVPTCLLPGS NQFLTTDDHS SAPAFPDFSP TPEMHIPGQV HSMLEIVQIE SMMEINNVND ASGVERLRVQ ISAQSDMDQL LFNIPLDIQ LEGPLRNTLL GNISRYYTHW SGSLEMTFMF CGSFMTTGKL IICYTPPGGS SPTDRMQAML ATHVVWDFGL Q SSITIIIP ...String:
GVPTCLLPGS NQFLTTDDHS SAPAFPDFSP TPEMHIPGQV HSMLEIVQIE SMMEINNVND ASGVERLRVQ ISAQSDMDQL LFNIPLDIQ LEGPLRNTLL GNISRYYTHW SGSLEMTFMF CGSFMTTGKL IICYTPPGGS SPTDRMQAML ATHVVWDFGL Q SSITIIIP WISGSHYRMF NTDAKAINAN VGYVTCFMQT NLVAPVGAAD QCYIVGMVAA KKDFNLRLMR DSPDIGQSAI LP EQA

-
Macromolecule #4: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: EV70, EV-70 / Strain: J670/71
Molecular weightTheoretical: 7.18676 KDa
SequenceString:
GAQVSRQQTG THENANVATG GSSITYNQIN FYKDSYAASA SKQDFSQDPS KFTEPVAEAL KAGAPVLK

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 150 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-16 / Number grids imaged: 2 / Number real images: 6698 / Average exposure time: 1.0 sec. / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 10524 / Details: autopicking using crYOLO
CTF correctionSoftware:
Namedetails
Gctfinitial CTF estimation
RELION (ver. 3.1)CTF refinement and correction

Details: RELION
Startup modelType of model: INSILICO MODEL
In silico model: SGD based initial model generation in RELION 3.1.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Software - 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: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 6390
DetailsMovie frames motion correction (MotionCor2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4mw8


Chain - Chain ID: A
RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 43
Output model

PDB-7opx:
CryoEM structure of human enterovirus 70 native virion

+
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