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- PDB-6zcl: Coxsackievirus B3 in complex with capsid binder compound 17 -

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Basic information

Entry
Database: PDB / ID: 6zcl
TitleCoxsackievirus B3 in complex with capsid binder compound 17
Components(capsid protein ...Capsid) x 4
KeywordsVIRUS / Enterovirus / coxackievirus B4 / capsid binder / inhibitor
Function / homology
Function and homology information


modulation by virus of host NIK/NF-kappaB signaling / induction by virus of host cytokine production / modulation by virus of host gene expression / suppression by virus of host translation initiation factor activity / suppression by virus of host MDA-5 activity / 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 / suppression by virus of host MAVS activity ...modulation by virus of host NIK/NF-kappaB signaling / induction by virus of host cytokine production / modulation by virus of host gene expression / suppression by virus of host translation initiation factor activity / suppression by virus of host MDA-5 activity / 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 / suppression by virus of host MAVS activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / positive stranded viral RNA replication / integral to membrane of host cell / pore formation by virus in membrane of host cell / protein complex oligomerization / 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 / membrane / ATP binding / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein like / Poliovirus 3A protein-like / Picornavirus 2B protein / Picornavirus core protein 2A / Peptidase C3, picornavirus core protein 2A / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) ...Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein like / Poliovirus 3A protein-like / Picornavirus 2B protein / Picornavirus core protein 2A / Peptidase C3, picornavirus core protein 2A / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / 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 / 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
Chem-FHK / MYRISTIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDomanska, A. / Flatt, J.W. / Butcher, S.J.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland315950 Finland
Sigrid Juselius FoundationNA 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

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Assembly

Deposited unit
A: capsid protein VP1
B: capsid protein VP2
C: capsid protein VP3
D: capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0416
Polymers91,3904
Non-polymers6512
Water0
1
A: capsid protein VP1
B: capsid protein VP2
C: capsid protein VP3
D: capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,522,442360
Polymers5,483,395240
Non-polymers39,047120
Water0
TypeNameSymmetry operationNumber
point symmetry operation60

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Components

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Capsid protein ... , 4 types, 4 molecules ABCD

#1: Protein capsid protein VP1 / / capsid protein VP1


Mass: 30268.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: capsid protein VP1 / Source: (natural) Coxsackievirus B3 (strain Nancy) / Cell line: Vero A
References: UniProt: P03313, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein capsid protein VP2 / / capsid protein VP2


Mass: 27604.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: capsid protein VP2 / Source: (natural) Coxsackievirus B3 (strain Nancy) / Cell line: Vero A
References: UniProt: P03313, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein capsid protein VP3 / / capsid protein VP3


Mass: 26067.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: capsid protein VP3 / Source: (natural) Coxsackievirus B3 (strain Nancy) / Cell line: Vero A
References: UniProt: P03313, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein capsid protein VP4 / / capsid protein VP4


Mass: 7449.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: myristoylated peptide, capsid protein VP4 / Source: (natural) Coxsackievirus B3 (strain Nancy) / Cell line: Vero A
References: UniProt: P03313, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

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Non-polymers , 2 types, 2 molecules

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


Mass: 422.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H14N2O6S / 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 B3 (strain Nancy) / Type: VIRUS
Details: Virus was grown in Vero A cells and purified in CsCl gradient
Entity ID: #1-#4 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Coxsackievirus B3 (strain Nancy) / Strain: Nancy
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: human
Virus shellName: icasaheadron / Diameter: 300 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Purified virus was mixed with compound 17 and incubated at room temperature for 30 min 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18626 / Symmetry type: POINT

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