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- EMDB-25776: Cryo-EM structure of Human Enterovirus D68 US/MO/14-18947 strain ... -

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Basic information

Entry
Database: EMDB / ID: EMD-25776
TitleCryo-EM structure of Human Enterovirus D68 US/MO/14-18947 strain in complex with inhibitor 11526093 (no/low occupancy-no inhibitor modeled)
Map dataEnterovirus D68 US/MO/14-18947 strain in complex with inhibitor 11526093 (no/low occupancy-no inhibitor modeled)
Sample
  • Virus: enterovirus D68
    • Protein or peptide: viral protein 1
    • Protein or peptide: viral protein 3
    • Protein or peptide: viral protein 2
    • Protein or peptide: viral protein 4
Function / homology
Function and homology information


: / 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...: / 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / 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 / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
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 ...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
Biological speciesenterovirus D68
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsFu J / Klose T / Kuhn RJ / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI011219 United States
CitationJournal: To Be Published
Title: Isoxazole-3-Carboxamide Derivatives of Pleconaril Destabilize the Viral Capsid of Enterovirus-D68
Authors: Lane T / Fu J / Sherry B / Tarbet B / Hurst BL / Riabova O / Kazakova E / Egorova A / Clarke P / Leser S / Frost J / Rudy M / Tyler K / Klose T / Kuhn RJ / Makarov V / Ekins S
History
DepositionDec 20, 2021-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJan 25, 2023-
Current statusJan 25, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25776.png

Downloads & links

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Map

FileDownload / File: emd_25776.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEnterovirus D68 US/MO/14-18947 strain in complex with inhibitor 11526093 (no/low occupancy-no inhibitor modeled)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 512 pix.
= 503.496 Å		0.98 Å/pix.
x 512 pix.
= 503.496 Å		0.98 Å/pix.
x 512 pix.
= 503.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98339 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.5528185 - 4.234597
Average (Standard dev.)0.003783331 (±0.19534972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 503.49567 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Enterovirus D68 US/MO/14-18947 strain in complex with inhibitor...

Fileemd_25776_half_map_1.map
AnnotationEnterovirus D68 US/MO/14-18947 strain in complex with inhibitor 11526093 (no/low occupancy-no inhibitor modeled)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Enterovirus D68 US/MO/14-18947 strain in complex with inhibitor...

Fileemd_25776_half_map_2.map
AnnotationEnterovirus D68 US/MO/14-18947 strain in complex with inhibitor 11526093 (no/low occupancy-no inhibitor modeled)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : enterovirus D68

EntireName: enterovirus D68
Components
  • Virus: enterovirus D68
    • Protein or peptide: viral protein 1
    • Protein or peptide: viral protein 3
    • Protein or peptide: viral protein 2
    • Protein or peptide: viral protein 4

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Supramolecule #1: enterovirus D68

SupramoleculeName: enterovirus D68 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 42789 / Sci species name: enterovirus D68 / Sci species strain: US/MO/14-18947 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: viral protein 1

MacromoleculeName: viral protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: enterovirus D68 / Strain: US/MO/14-18947
Molecular weightTheoretical: 32.819207 KDa
SequenceString: IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKDHT SSTARADKN FFKWTINTRS FVQLRRKLEL FTYLRFDAEI TILTTVAVNG SGNNTYVGLP DLTLQAMFVP TGALTPEKQD S FHWQSGSN ...String:
IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKDHT SSTARADKN FFKWTINTRS FVQLRRKLEL FTYLRFDAEI TILTTVAVNG SGNNTYVGLP DLTLQAMFVP TGALTPEKQD S FHWQSGSN ASVFFKISDP PARITIPFMC INSAYSVFYD GFAGFEKNGL YGINPADTIG NLCVRIVNEH QPVGFTVTVR VY MKPKHIK AWAPRPPRTL PYMSIANANY KGKERAPNAL SAIIGNRDSV KTMPHNIVN

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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 / Strain: US/MO/14-18947
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

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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 / Strain: US/MO/14-18947
Molecular weightTheoretical: 26.573094 KDa
SequenceString: SDRVLQLKLG NSAIVTQEAA NYCCAYGEWP NYLPDHEAVA IDKPTQPETA TDRFYTLKSV KWETGSTGWW WKLPDALNNI GMFGQNVQH HYLYRSGFLI HVQCNATKFH QGALLVVAIP EHQRGAHNTN TSPGFDDIMK GEEGGTFNHP YVLDDGTSLA C ATIFPHQW ...String:
SDRVLQLKLG NSAIVTQEAA NYCCAYGEWP NYLPDHEAVA IDKPTQPETA TDRFYTLKSV KWETGSTGWW WKLPDALNNI GMFGQNVQH HYLYRSGFLI HVQCNATKFH QGALLVVAIP EHQRGAHNTN TSPGFDDIMK GEEGGTFNHP YVLDDGTSLA C ATIFPHQW INLRTNNSAT IVLPWMNAAP MDFPLRHNQW TLAIIPVVPL GTRTTSSMVP ITVSIAPMCC EFNGLRHAIT

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Macromolecule #4: viral protein 4

MacromoleculeName: viral protein 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: enterovirus D68 / Strain: US/MO/14-18947
Molecular weightTheoretical: 7.33696 KDa
SequenceString:
GAQVTRQQTG THENANIATN GSHITYNQIN FYKDSYAASA SKQDFSQDPS KFTEPVVEGL KAGAPVLK

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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: 8
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 64000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 36.06 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 255145
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6csg

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7taj:
Cryo-EM structure of Human Enterovirus D68 US/MO/14-18947 strain in complex with inhibitor 11526093 (no/low occupancy-no inhibitor modeled)

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