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- PDB-9fp5: Coxsackievirus A9 bound with CL213. -

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Basic information

Entry
Database: PDB / ID: 9fp5
TitleCoxsackievirus A9 bound with CL213.
Components(Capsid protein ...) x 4
KeywordsVIRUS / Antiviral / capsid stabilizer / hydrophobic pocket / cryoEM
Function / homology
Function and homology information


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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity ...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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / 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) / 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
MYRISTIC ACID / PALMITIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus A9
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsPlavec, Z. / Butcher, S.J. / Mitchell, C. / Buckner, C.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland315950 Finland
Sigrid Juselius Foundation95-7202-38 Finland
Jane and Aatos Erkko Foundation Finland
Citation
Journal: J Med Chem / Year: 2024
Title: SAR Analysis of Novel Coxsackie virus A9 Capsid Binders.
Authors: Chiara Tammaro / Zlatka Plavec / Laura Myllymäki / Cristopher Mitchell / Sara Consalvi / Mariangela Biava / Alessia Ciogli / Aušra Domanska / Valtteri Leppilampi / Cienna Buckner / Simone ...Authors: Chiara Tammaro / Zlatka Plavec / Laura Myllymäki / Cristopher Mitchell / Sara Consalvi / Mariangela Biava / Alessia Ciogli / Aušra Domanska / Valtteri Leppilampi / Cienna Buckner / Simone Manetto / Pietro Sciò / Antonio Coluccia / Mira Laajala / Giulio M Dondio / Chiara Bigogno / Varpu Marjomäki / Sarah J Butcher / Giovanna Poce /
Abstract: Enterovirus infections are common in humans, yet there are no approved antiviral treatments. In this study we concentrated on inhibition of one of the (EV-B), namely Coxsackievirus A9 (CVA9), using ...Enterovirus infections are common in humans, yet there are no approved antiviral treatments. In this study we concentrated on inhibition of one of the (EV-B), namely Coxsackievirus A9 (CVA9), using a combination of medicinal chemistry, virus inhibition assays, structure determination from cryogenic electron microscopy and molecular modeling, to determine the structure activity relationships for a promising class of novel -phenylbenzylamines. Of the new 29 compounds synthesized, 10 had half maximal effective concentration (EC) values between 0.64-10.46 μM, and of these, 7 had 50% cytotoxicity concentration (CC) values higher than 200 μM. In addition, this new series of compounds showed promising physicochemical properties and act through capsid stabilization, preventing capsid expansion and subsequent release of the genome.
#1: Journal: Protein Sci / Year: 2021
Title: UCSF ChimeraX: Structure visualization for researchers, educators, and developers.
Authors: Eric F Pettersen / Thomas D Goddard / Conrad C Huang / Elaine C Meng / Gregory S Couch / Tristan I Croll / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) ...UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic "undo" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax.
History
DepositionJun 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)96,9266
Polymers96,4424
Non-polymers4852
Water00
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)5,815,587360
Polymers5,786,499240
Non-polymers29,088120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

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

#1: Protein Capsid protein VP1 / P1D / Virion protein 1


Mass: 33869.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A9 / Cell line: GMK / Strain: Griggs / Tissue: kidney / References: UniProt: P21404
#2: Protein Capsid protein VP2 / P1B / Virion protein 2


Mass: 28885.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A9 / Cell line: GMK / Strain: Griggs / Tissue: kidney / References: UniProt: P21404
#3: Protein Capsid protein VP3 / P1C / Virion protein 3


Mass: 26335.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A9 / Cell line: GMK / Strain: Griggs / Tissue: kidney / References: UniProt: P21404
#4: Protein Capsid protein VP4 / P1A / Virion protein 4


Mass: 7352.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A9 / Cell line: GMK / Strain: Griggs / Tissue: kidney / References: UniProt: P21404

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical ChemComp-MYR / 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
Has protein modificationN

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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: Human coxsackievirus A9 (strain Griggs) / Type: VIRUS
Details: Coxsackievirus A9 was propagated on green monkey kidney cells and purified on a sucrose gradient.
Entity ID: #1-#4 / Source: NATURAL
Molecular weightValue: 8 MDa / Experimental value: NO
Source (natural)Organism: Human coxsackievirus A9 (strain Griggs) / Strain: Griggs
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: icosahedral capsid / Diameter: 300 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.2
SpecimenConc.: 0.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: CL213 stock solution in DMSO was diluted in PBS containing 2mM MgCl2 for final concentration of 1 mg/ml. 10 ul of purified CVA9 with the concentration of 0.7 mg/ml was mixed with 4 ul of ...Details: CL213 stock solution in DMSO was diluted in PBS containing 2mM MgCl2 for final concentration of 1 mg/ml. 10 ul of purified CVA9 with the concentration of 0.7 mg/ml was mixed with 4 ul of CL213 diluted in PBS containing 2mM MgCl2 to a final concentration of CL213 of 0.28 mg/ml. The virus-compound mixture was incubated for 1 hour in 37 C. The final molar concentration of the virus was approximately 71 nM and CL213 concentration was approximately 7.8 mM.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 295 K
Details: Sample was incubated for 15 s on the grid before blotted from the front for 1.5 s.

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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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1Scipion3.0.8particle selectionManual particle picking was done with xmipp3 and after picking 705 particles, automatic picking with xmipp3 was used. Relion3 (Zivanov et al., 2018) was used for particle extraction with a box size of 400 pixel. In total, 216 957 particles were extracted from the data set.
4Scipion3.0.8CTF correctionContrast transfer function (CTF) was evaluated with CTFFIND4 (Rohou & Grigorieff, 2015) with defocus ranging between 5000 and 50 000 and resolution range of 5 and 50.
7UCSF ChimeraX1.5model fitting
8Coot0.9.8.1model fitting
10Scipion3.0.8initial Euler assignment
11Scipion3.0.8final Euler assignment
12Scipion3.0.8classificationOne high quality class containing 90 678 well- resolved particles was chosen for further analysis.
13Scipion3.0.83D reconstruction
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 216957
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90678 / Symmetry type: POINT
Atomic model buildingB value: 70
Atomic model buildingPDB-ID: 8AT5

8at5


Accession code: 8AT5 / Source name: PDB / Type: experimental model

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