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- PDB-6zck: Coxsackievirus B4 in complex with capsid binder compound 48 -

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Entry
Database: PDB / ID: 6zck
TitleCoxsackievirus B4 in complex with capsid binder compound 48
Components(Genome polyprotein) x 4
KeywordsVIRUS / Enterovirus / Coxsackievirus B4 / Inhibitor / Capsid Binder
Function / homology
Function and homology information


suppression by virus of host RIG-I activity / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / integral to membrane of host cell / pore formation by virus in membrane of host cell ...suppression by virus of host RIG-I activity / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / integral to membrane of host cell / pore formation by virus in membrane of host cell / protein complex oligomerization / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / suppression by virus of host gene expression / ion channel activity / induction by virus of host autophagy / DNA replication / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / transcription, DNA-templated / virion attachment to host cell / host cell nucleus / structural molecule activity / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Picornavirus core protein 2A / Peptidase C3, picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus coat protein (VP4) / Picornavirus coat protein VP4 ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Picornavirus core protein 2A / Peptidase C3, picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus coat protein (VP4) / Picornavirus coat protein VP4 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 3C cysteine protease (picornain 3C) / Peptidase C3A/C3B, picornaviral / picornavirus capsid protein / Picornavirus capsid / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RNA helicase / Helicase, superfamily 3, single-stranded DNA/RNA virus / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, C-terminal 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 / Reverse transcriptase/Diguanylate cyclase 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
MYRISTIC ACID / Chem-QFW / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFlatt, J.W. / Domanska, A. / Butcher, S.J.
Funding support Finland, 2items
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, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9026
Polymers91,2724
Non-polymers6302
Water0
1
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Genome polyprotein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,514,099360
Polymers5,476,311240
Non-polymers37,788120
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation59

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Genome polyprotein


Mass: 30685.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B4 (strain E2) / Cell line: BGM
References: UniProt: Q8V639, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein Genome polyprotein


Mass: 27708.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B4 (strain E2) / Cell line: BGM
References: UniProt: Q8V639, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein Genome polyprotein


Mass: 26444.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B4 (strain E2) / Cell line: BGM
References: UniProt: Q8V639, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein Genome polyprotein


Mass: 6434.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus B4 (strain E2) / Cell line: BGM
References: UniProt: Q8V639, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-QFW / 2-oxidanyl-4-[(6-propoxynaphthalen-2-yl)sulfonylamino]benzoic acid


Mass: 401.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19NO6S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Coxsackievirus B4 (strain E2) / Type: VIRUS
Details: Virus harvested in BGM cells and purified in CsCl gradient.
Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Coxsackievirus B4 (strain E2)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Icosahedron / Diameter: 300 nm / Triangulation number (T number): 3
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHepesC8H18N2O4S1
2150 mMSodium chlorideNaClSodium chloride1
32 mMMagnesium chlorideMgCl21
42 mMCalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: purified virus mixed with compound 48, incubated at room temperature for 30 minutes before plunging.
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 47 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13252 / Symmetry type: POINT

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