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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


: / symbiont-mediated perturbation of host gene expression / 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 ...: / symbiont-mediated perturbation of host gene expression / 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 / 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 / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / 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
Revision 1.1May 31, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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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
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: capsid protein VP1
B: capsid protein VP2
C: capsid protein VP3
D: capsid protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 460 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)460,20330
Polymers456,95020
Non-polymers3,25410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: capsid protein VP1
B: capsid protein VP2
C: capsid protein VP3
D: capsid protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 552 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)552,24436
Polymers548,33924
Non-polymers3,90512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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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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