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- EMDB-11165: Coxsackievirus B4 in complex with capsid binder compound 48 -

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Basic information

Entry
Database: EMDB / ID: EMD-11165
TitleCoxsackievirus B4 in complex with capsid binder compound 48
Map dataCoxsackievirus B4 in complex with capsid binder compound 48
Sample
  • Virus: Coxsackievirus B4 (strain E2)
    • 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-[(6-propoxynaphthalen-2-yl)sulfonylamino]benzoic acid
Function / homology
Function and homology information


: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / 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 / ribonucleoside triphosphate phosphatase activity ...: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / 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 / ribonucleoside triphosphate phosphatase activity / 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 / RNA helicase activity / DNA replication / 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 / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / 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) ...Picornavirus coat protein VP4 superfamily / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesCoxsackievirus B4 (strain E2)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFlatt JW / Domanska A / Butcher SJ
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-
UpdateMay 31, 2023-
Current statusMay 31, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00928
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00928
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zck
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zck
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11165.png

Downloads & links

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Map

FileDownload / File: emd_11165.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCoxsackievirus B4 in complex with capsid binder compound 48
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.00928 / Movie #1: 0.00928
Minimum - Maximum-0.035159986 - 0.07784694
Average (Standard dev.)0.001138117 (±0.0055316053)
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-0.0350.0780.001

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Supplemental data

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Sample components

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Entire : Coxsackievirus B4 (strain E2)

EntireName: Coxsackievirus B4 (strain E2)
Components
  • Virus: Coxsackievirus B4 (strain E2)
    • 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-[(6-propoxynaphthalen-2-yl)sulfonylamino]benzoic acid

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Supramolecule #1: Coxsackievirus B4 (strain E2)

SupramoleculeName: Coxsackievirus B4 (strain E2) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Virus harvested in BGM cells and purified in CsCl gradient.
NCBI-ID: 103905 / Sci species name: Coxsackievirus B4 (strain E2) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Icosahedron / Diameter: 300.0 Å / T number (triangulation number): 3

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B4 (strain E2) / Strain: E2
Molecular weightTheoretical: 30.685498 KDa
SequenceString: MGRVADTIAR GPSNSEQIPA LTAVETGHTS QVDPSDTMQT RHVHNYHSRS ESSIENFLCR SACVIYIKYS SAESNNLKRY AEWVINTRQ VAQLRRKMEM FTYIRCDMEL TFVITSHQEM STATNSDVPV QTHQIMYVPP GGPVPTSVND YVWQTSTNPS I FWTEGNAP ...String:
MGRVADTIAR GPSNSEQIPA LTAVETGHTS QVDPSDTMQT RHVHNYHSRS ESSIENFLCR SACVIYIKYS SAESNNLKRY AEWVINTRQ VAQLRRKMEM FTYIRCDMEL TFVITSHQEM STATNSDVPV QTHQIMYVPP GGPVPTSVND YVWQTSTNPS I FWTEGNAP PRMSIPFMSI GNAYTMFYDG WSNFSRDGIY GYNSLNNMGT IYARHVNDSS PGGLTSTIRI YFKPKHVKAY VP RPPRLCQ YKKAKNVNFD VEAVTTERAS LVTT

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Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B4 (strain E2) / Strain: E2
Molecular weightTheoretical: 27.70807 KDa
SequenceString: SDRVRSITLG NSTITTQECA NVVVGYGVWP DYLSDEEATA EDQPTQPDVA TCRFYTLNSV KWEMQSAGWW WKFPDALSEM GLFGQNMQY HYLGRSGYTI HVQCNASKFH QGCLLVVCVP EAEMGCTNAE NAPTYGDLCG GETAKQFEQN AVTGETAVQT A VCNAGMGV ...String:
SDRVRSITLG NSTITTQECA NVVVGYGVWP DYLSDEEATA EDQPTQPDVA TCRFYTLNSV KWEMQSAGWW WKFPDALSEM GLFGQNMQY HYLGRSGYTI HVQCNASKFH QGCLLVVCVP EAEMGCTNAE NAPTYGDLCG GETAKQFEQN AVTGETAVQT A VCNAGMGV GVGNLTIYPH QWINLRTNNS ATIVMPYINS VPMDNMFRHN NFTLMIIPFA PLDYVTGASS YIPITVTVAP MS AEYNGLR LAGHQ

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Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B4 (strain E2) / Strain: E2
Molecular weightTheoretical: 26.44416 KDa
SequenceString: GLPTMLTPGS TQFLTSDDFQ SPSAMPQFDV TPEMNIPGQV RNLMEIAEVD SVVPINNLQA NLKTMEAYRV QVRSTDEMGG QIFGFPLQP GASSVLQRTL LGEILNYYTH WSGSLKLTFV FCGSAMATGK FLLAYSPPGA GAPDSRKNAM LGTHVIWDVG L QSSCVLCV ...String:
GLPTMLTPGS TQFLTSDDFQ SPSAMPQFDV TPEMNIPGQV RNLMEIAEVD SVVPINNLQA NLKTMEAYRV QVRSTDEMGG QIFGFPLQP GASSVLQRTL LGEILNYYTH WSGSLKLTFV FCGSAMATGK FLLAYSPPGA GAPDSRKNAM LGTHVIWDVG L QSSCVLCV PWISQTHYRY VVDDKYTASG FISCWYQTNV IVPAEAQKSC YIMCFVSACN DFSVRMLRDT QFIKQDTFYQ

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Macromolecule #4: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B4 (strain E2) / Strain: E2
Molecular weightTheoretical: 7.499235 KDa
SequenceString:
MGAQVSTQKT GAHETSLSAS GNSIIHYTNI NYYKDAASNS ANRQDFTQDP SKFTEPVKDV MIKSLPALN

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Macromolecule #5: 4-[(6-propoxynaphthalen-2-yl)sulfonylamino]benzoic acid

MacromoleculeName: 4-[(6-propoxynaphthalen-2-yl)sulfonylamino]benzoic acid
type: ligand / ID: 5 / Number of copies: 1 / Formula: QFW
Molecular weightTheoretical: 385.434 Da
Chemical component information

ChemComp-QFW:
4-[(6-propoxynaphthalen-2-yl)sulfonylamino]benzoic acid

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHepes
150.0 mMNaClSodium chlorideSodium chloride
2.0 mMMgCl2Magnesium chloride
2.0 mMCaCl2Calcium chloride
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: Ted Pella product No. 01824
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Detailspurified virus mixed with compound 48, incubated at room temperature for 30 minutes before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 13252

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