[English] 日本語
Yorodumi
- EMDB-11166: Coxsackievirus B3 in complex with capsid binder compound 17 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11166
TitleCoxsackievirus B3 in complex with capsid binder compound 17
Map dataCoxsackie B3 virion in complex with compound 17
Sample
  • Virus: Coxsackievirus B3 (strain Nancy)
    • 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: 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid
  • Ligand: MYRISTIC ACID
KeywordsEnterovirus / coxackievirus B4 / capsid binder / inhibitor / VIRUS
Function / homology
Function and homology information


symbiont-mediated perturbation of host transcription / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS 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 ...symbiont-mediated perturbation of host transcription / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS 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 NF-kappaB cascade / 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 / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein VP4 superfamily / 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 superfamily / 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. / 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 speciesCoxsackievirus B3 (strain Nancy)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDomanska A / Flatt JW
Funding support Finland, 2 items
OrganizationGrant numberCountry
Academy of Finland315950 Finland
Sigrid Juselius Foundation Finland
CitationJournal: Commun Biol / Year: 2021
Title: Identification of a conserved virion-stabilizing network inside the interprotomer pocket of enteroviruses.
Authors: Justin W Flatt / Aušra Domanska / Alma L Seppälä / Sarah J Butcher /
Abstract: Enteroviruses pose a persistent and widespread threat to human physical health, with no specific treatments available. Small molecule capsid binders have the potential to be developed as antivirals ...Enteroviruses pose a persistent and widespread threat to human physical health, with no specific treatments available. Small molecule capsid binders have the potential to be developed as antivirals that prevent virus attachment and entry into host cells. To aid with broad-range drug development, we report here structures of coxsackieviruses B3 and B4 bound to different interprotomer-targeting capsid binders using single-particle cryo-EM. The EM density maps are beyond 3 Å resolution, providing detailed information about interactions in the ligand-binding pocket. Comparative analysis revealed the residues that form a conserved virion-stabilizing network at the interprotomer site, and showed the small molecule properties that allow anchoring in the pocket to inhibit virus disassembly.
History
DepositionJun 11, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zcl
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11166.png

Downloads & links

-
Map

FileDownload / File: emd_11166.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCoxsackie B3 virion in complex with compound 17
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 420 pix.
= 445.2 Å		1.06 Å/pix.
x 420 pix.
= 445.2 Å		1.06 Å/pix.
x 420 pix.
= 445.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.07034672 - 0.12498104
Average (Standard dev.)0.0006518885 (±0.006750057)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 445.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z445.200445.200445.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.0700.1250.001

-
Supplemental data

-
Sample components

-
Entire : Coxsackievirus B3 (strain Nancy)

EntireName: Coxsackievirus B3 (strain Nancy)
Components
  • Virus: Coxsackievirus B3 (strain Nancy)
    • 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: 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid
  • Ligand: MYRISTIC ACID

-
Supramolecule #1: Coxsackievirus B3 (strain Nancy)

SupramoleculeName: Coxsackievirus B3 (strain Nancy) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Virus was grown in Vero A cells and purified in CsCl gradient
NCBI-ID: 103903 / Sci species name: Coxsackievirus B3 (strain Nancy) / Sci species strain: Nancy / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: human (human)
Virus shellShell ID: 1 / Name: icasaheadron / Diameter: 300.0 Å / T number (triangulation number): 3

-
Macromolecule #1: capsid protein VP1

MacromoleculeName: capsid protein VP1 / type: protein_or_peptide / ID: 1 / Details: capsid protein VP1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus B3 (strain Nancy)
Molecular weightTheoretical: 30.26893 KDa
SequenceString: RVADTVGTGP TNSEAIPALT AAETGHTSQV VPGDTMQTRH VKNYHSRSES TIENFLCRSA CVYFTEYKNS GAKRYAEWVL TPRQAAQLR RKLEFFTYVR FDLELTFVIT STQQPSTTQN QDAQILTHQI MYVPPGGPVP DKVDSYVWQT STNPSVFWTE G NAPPRMSI ...String:
RVADTVGTGP TNSEAIPALT AAETGHTSQV VPGDTMQTRH VKNYHSRSES TIENFLCRSA CVYFTEYKNS GAKRYAEWVL TPRQAAQLR RKLEFFTYVR FDLELTFVIT STQQPSTTQN QDAQILTHQI MYVPPGGPVP DKVDSYVWQT STNPSVFWTE G NAPPRMSI PFLSIGNAYS NFYDGWSEFS RNGVYGINTL NNMGTLYARH VNAGSTGPIK STIRIYFKPK HVKAWIPRPP RL CQYEKAK NVNFQPSGVT TTRQSITTMT NT

UniProtKB: Genome polyprotein

-
Macromolecule #2: capsid protein VP2

MacromoleculeName: capsid protein VP2 / type: protein_or_peptide / ID: 2 / Details: capsid protein VP2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus B3 (strain Nancy)
Molecular weightTheoretical: 27.604205 KDa
SequenceString: SDRARSITLG NSTITTQECA NVVVGYGVWP DYLKDSEATA EDQPTQPDVA TCRFYTLDSV QWQKTSPGWW WKLPDALSNL GLFGQNMQY HYLGRTGYTV HVQCNASKFH QGCLLVVCVP EAEMGCATLD NTPSSAELLG GDTAKEFADK PVASGSNKLV Q RVVYNAGM ...String:
SDRARSITLG NSTITTQECA NVVVGYGVWP DYLKDSEATA EDQPTQPDVA TCRFYTLDSV QWQKTSPGWW WKLPDALSNL GLFGQNMQY HYLGRTGYTV HVQCNASKFH QGCLLVVCVP EAEMGCATLD NTPSSAELLG GDTAKEFADK PVASGSNKLV Q RVVYNAGM GVGVGNLTIF PHQWINLRTN NSATIVMPYT NSVPMDNMFR HNNVTLMVIP FVPLDYCPGS TTYVPITVTI AP MCAEYNG LRLAG

UniProtKB: Genome polyprotein

-
Macromolecule #3: capsid protein VP3

MacromoleculeName: capsid protein VP3 / type: protein_or_peptide / ID: 3 / Details: capsid protein VP3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus B3 (strain Nancy)
Molecular weightTheoretical: 26.067596 KDa
SequenceString: GLPTMNTPGS CQFLTSDDFQ SPSAMPQYDV TPEMRIPGEV KNLMEIAEVD SVVPVQNVGE KVNSMEAYQI PVRSNEGSGT QVFGFPLQP GYSSVFSRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTKRVDAM LGTHVIWDVG L QSSCVLCI ...String:
GLPTMNTPGS CQFLTSDDFQ SPSAMPQYDV TPEMRIPGEV KNLMEIAEVD SVVPVQNVGE KVNSMEAYQI PVRSNEGSGT QVFGFPLQP GYSSVFSRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GAPTKRVDAM LGTHVIWDVG L QSSCVLCI PWISQTHYRF VASDEYTAGG FITCWYQTNI VVPADAQSSC YIMCFVSACN DFSVRLLKDT PFISQQNFF

UniProtKB: Genome polyprotein

-
Macromolecule #4: capsid protein VP4

MacromoleculeName: capsid protein VP4 / type: protein_or_peptide / ID: 4 / Details: myristoylated peptide, capsid protein VP4 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Coxsackievirus B3 (strain Nancy)
Molecular weightTheoretical: 7.449181 KDa
SequenceString:
GAQVSTQKTG AHETRLNASG NSIIHYTNIN YYKDAASNSA NRQDFTQDPG KFTEPVKDIM IKSLPALN

UniProtKB: Genome polyprotein

-
Macromolecule #5: 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]b...

MacromoleculeName: 4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid
type: ligand / ID: 5 / Number of copies: 1 / Formula: FHK
Molecular weightTheoretical: 422.411 Da
Chemical component information

ChemComp-FHK:
4-[[4-[1,3-bis(oxidanylidene)isoindol-2-yl]phenyl]sulfonylamino]benzoic acid

-
Macromolecule #6: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
DetailsPurified virus was mixed with compound 17 and incubated at room temperature for 30 min before plunging

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18626
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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