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- EMDB-44072: EV-D68 in complex with inhibitor Jun11-69-5 -

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Basic information

Entry
Database: EMDB / ID: EMD-44072
TitleEV-D68 in complex with inhibitor Jun11-69-5
Map dataEV-D68 in complex with inhibitor Jun11-69-5
Sample
  • Virus: EV-D68 US/MO/14-18947 (virus)
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: viral protein 3
    • Protein or peptide: viral protein 2
    • Protein or peptide: Capsid protein VP4
  • Ligand: (5M)-5-{8-[({4-[(propan-2-yl)oxy]phenyl}methyl)amino]quinolin-4-yl}pyridine-2-carbonitrile
KeywordsEV-D68 / Inhibitor / Structural Genomics / VIRAL PROTEIN
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 / cysteine-type peptidase activity / protein sequestering 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 / cysteine-type peptidase activity / protein sequestering 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 / monoatomic ion transmembrane transport / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / RNA helicase activity / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host gene expression / 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 / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / 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 / EV-D68 US/MO/14-18947 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsKlose T / Kuhn RJ / Jun W
Funding support United States, 2 items
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 MJ / Klose T / Tan H / Wu X / Anderson JS / Yu W / Jadhav P / Zhang Q / Clarke P / Kuhn RJ / Tyler KL / Wang J
History
DepositionMar 13, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44072.png

Downloads & links

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Map

FileDownload / File: emd_44072.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEV-D68 in complex with inhibitor Jun11-69-5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 512 pix.
= 571.04 Å		1.12 Å/pix.
x 512 pix.
= 571.04 Å		1.12 Å/pix.
x 512 pix.
= 571.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11531 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.64
Minimum - Maximum-2.8325312 - 4.5400014
Average (Standard dev.)0.001962081 (±0.18925507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 571.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_44072_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_44072_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : EV-D68 US/MO/14-18947

EntireName: EV-D68 US/MO/14-18947 (virus)
Components
  • Virus: EV-D68 US/MO/14-18947 (virus)
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: viral protein 3
    • Protein or peptide: viral protein 2
    • Protein or peptide: Capsid protein VP4
  • Ligand: (5M)-5-{8-[({4-[(propan-2-yl)oxy]phenyl}methyl)amino]quinolin-4-yl}pyridine-2-carbonitrile

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Supramolecule #1: EV-D68 US/MO/14-18947

SupramoleculeName: EV-D68 US/MO/14-18947 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 42789 / Sci species name: EV-D68 US/MO/14-18947 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: enterovirus D68
Molecular weightTheoretical: 34.242734 KDa
SequenceString: LDHLHAAEAA YQIESIIKTA TDTVKSEINA ELGVVPSLNA VETGATSNTE PEEAIQTRTV INQHGVSETL VENFLSRAAL VSKRSFEYK DHTSSTARAD KNFFKWTINT RSFVQLRRKL ELFTYLRFDA EITILTTVAV NGSGNNTYVG LPDLTLQAMF V PTGALTPE ...String:
LDHLHAAEAA YQIESIIKTA TDTVKSEINA ELGVVPSLNA VETGATSNTE PEEAIQTRTV INQHGVSETL VENFLSRAAL VSKRSFEYK DHTSSTARAD KNFFKWTINT RSFVQLRRKL ELFTYLRFDA EITILTTVAV NGSGNNTYVG LPDLTLQAMF V PTGALTPE KQDSFHWQSG SNASVFFKIS DPPARITIPF MCINSAYSVF YDGFAGFEKN GLYGINPADT IGNLCVRIVN EH QPVGFTV TVRVYMKPKH IKAWAPRPPR TLPYMSIANA NYKGKERAPN ALSAIIGNRD SVKTMPHNIV NT

UniProtKB: Genome polyprotein

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Macromolecule #2: viral protein 3

MacromoleculeName: viral protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: enterovirus D68
Molecular weightTheoretical: 27.112814 KDa
SequenceString: GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMAAGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSVTLIIP ...String:
GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMAAGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSVTLIIP WISGSHYRMF NNDAKSTNAN VGYVTCFMQT NLIVPSESSD TCSLIGFIAA KDDFSLRLMR DSPDIGQLDH LH AAEAAYQ

UniProtKB: Genome polyprotein

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Macromolecule #3: viral protein 2

MacromoleculeName: viral protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: enterovirus D68
Molecular weightTheoretical: 27.567135 KDa
SequenceString: SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETGSTGWWW KLPDALNNI GMFGQNVQHH YLYRSGFLIH VQCNATKFHQ GALLVVAIPE HQRGAHNTNT SPGFDDIMKG EEGGTFNHPY V LDDGTSLA ...String:
SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETGSTGWWW KLPDALNNI GMFGQNVQHH YLYRSGFLIH VQCNATKFHQ GALLVVAIPE HQRGAHNTNT SPGFDDIMKG EEGGTFNHPY V LDDGTSLA CATIFPHQWI NLRTNNSATI VLPWMNAAPM DFPLRHNQWT LAIIPVVPLG TRTTSSMVPI TVSIAPMCCE FN GLRHAIT Q

UniProtKB: Genome polyprotein

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Macromolecule #4: Capsid protein VP4

MacromoleculeName: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: enterovirus D68
Molecular weightTheoretical: 7.468157 KDa
SequenceString:
MGAQVTRQQT GTHENANIAT NGSHITYNQI NFYKDSYAAS ASKQDFSQDP SKFTEPVVEG LKAGAPVLK

UniProtKB: Genome polyprotein

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Macromolecule #5: (5M)-5-{8-[({4-[(propan-2-yl)oxy]phenyl}methyl)amino]quinolin-4-y...

MacromoleculeName: (5M)-5-{8-[({4-[(propan-2-yl)oxy]phenyl}methyl)amino]quinolin-4-yl}pyridine-2-carbonitrile
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1AIF
Molecular weightTheoretical: 394.468 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6860 / Average exposure time: 3.12 sec. / Average electron dose: 35.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 317890
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7tag


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9b1a:
EV-D68 in complex with inhibitor Jun11-69-5

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