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- PDB-9b19: EV-D68 in complex with inhibitor Jun11-54-1 -

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Basic information

Entry
Database: PDB / ID: 9b19
TitleEV-D68 in complex with inhibitor Jun11-54-1
Components
  • Capsid protein VP1
  • Capsid protein VP4
  • viral protein 2
  • viral protein 3
KeywordsVIRAL PROTEIN / EV-D68 / Inhibitor
Function / homology
Function and homology information


symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / host cell membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / protein sequestering activity / cysteine-type peptidase activity / helicase 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 ...symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway / host cell membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / protein sequestering activity / cysteine-type peptidase activity / helicase 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 / viral capsid / nucleoside-triphosphate phosphatase / channel activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host NF-kappaB cascade / monoatomic ion transmembrane transport / host cell cytoplasm / RNA helicase activity / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase activity / 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 / cytoplasm
Similarity search - Function
Picornavirus coat protein / 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 / 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
: / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesenterovirus D68
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsKlose, T. / Kuhn, R.J. / Jun, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI157046 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI147325 United States
CitationJournal: To Be Published
Title: Design of enterovirus D68 capsid inhibitors with in vivo antiviral efficacy
Authors: Li, K. / Rudy, M.J. / Klose, T. / Tan, H. / Wu, X. / Anderson, J.S. / Yu, W. / Jadhav, P. / Zhang, Q. / Clarke, P. / Kuhn, R.J. / Tyler, K.L. / Wang, J.
History
DepositionMar 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Other / Structure summary
Category: audit_author / em_admin ...audit_author / em_admin / em_author_list / pdbx_SG_project / struct_keywords
Item: _em_admin.last_update / _struct_keywords.text
Revision 1.1Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Experimental summary / Structure summary / Data content type: EM metadata / EM metadata / EM metadata / Category: em_admin / em_author_list / struct_keywords / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: viral protein 3
C: viral protein 2
D: Capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8085
Polymers96,3914
Non-polymers4181
Water00
1
A: Capsid protein VP1
B: viral protein 3
C: viral protein 2
D: Capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,808,502300
Polymers5,783,450240
Non-polymers25,05160
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: viral protein 3
C: viral protein 2
D: Capsid protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 484 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)484,04225
Polymers481,95420
Non-polymers2,0885
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: viral protein 3
C: viral protein 2
D: Capsid protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 581 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)580,85030
Polymers578,34524
Non-polymers2,5056
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein VP1


Mass: 34242.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) enterovirus D68
References: UniProt: A0A097BW12, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein viral protein 3 / VP3


Mass: 27112.814 Da / Num. of mol.: 1 / Fragment: UNP residues 318-564 / Source method: isolated from a natural source / Source: (natural) enterovirus D68 / References: UniProt: A0A097BW12
#3: Protein viral protein 2 / VP2


Mass: 27567.135 Da / Num. of mol.: 1 / Fragment: UNP residues 70-317 / Source method: isolated from a natural source / Source: (natural) enterovirus D68 / References: UniProt: A0A0A7X639
#4: Protein Capsid protein VP4


Mass: 7468.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) enterovirus D68 / References: UniProt: Q68T42
#5: Chemical ChemComp-A1AIE / N-{(4M)-4-[5-(aminomethyl)thiophen-2-yl]quinolin-8-yl}-4-[(propan-2-yl)oxy]benzamide


Mass: 417.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23N3O2S / Feature type: SUBJECT OF INVESTIGATION
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: EV-D68 US/MO/14-18947 / Type: VIRUS / Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: EV-D68 US/MO/14-18947 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K

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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 magnification: 64000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.12 sec. / Electron dose: 35.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7663
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7ISOLDEmodel fitting
8UCSF ChimeraXmodel fitting
9Cootmodel fitting
11PHENIXmodel refinement
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
14cryoSPARCclassification
15cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 160815 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 7tag

7tag


Accession code: 7tag / Source name: PDB / Type: experimental model

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