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- EMDB-9055: CryoEM structure of human enterovirus D68 expanded 1 particle (pH... -

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Basic information

Entry
Database: EMDB / ID: EMD-9055
TitleCryoEM structure of human enterovirus D68 expanded 1 particle (pH 6.5, 4 degrees Celsius, 3 min)
Map datasharpened map in which the inner density is masked out
Sample
  • Virus: Enterovirus D68
    • Protein or peptide: Viral protein 1
    • Protein or peptide: Viral protein 2
    • Protein or peptide: Viral protein 3
    • 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 / symbiont-mediated suppression of host gene expression / viral capsid ...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 / symbiont-mediated suppression of host gene expression / viral capsid / nucleoside-triphosphate phosphatase / channel activity / peptidase activity / monoatomic ion transmembrane transport / host cell cytoplasm / RNA helicase activity / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / symbiont entry into host cell / 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 / metal ion binding / cytoplasm
Similarity search - Function
Picornavirus coat protein VP4 superfamily / 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 superfamily / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsLiu Y / Rossmann MG
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Molecular basis for the acid-initiated uncoating of human enterovirus D68.
Authors: Yue Liu / Ju Sheng / Arno L W van Vliet / Geeta Buda / Frank J M van Kuppeveld / Michael G Rossmann /
Abstract: Enterovirus D68 (EV-D68) belongs to a group of enteroviruses that contain a single positive-sense RNA genome surrounded by an icosahedral capsid. Like common cold viruses, EV-D68 mainly causes ...Enterovirus D68 (EV-D68) belongs to a group of enteroviruses that contain a single positive-sense RNA genome surrounded by an icosahedral capsid. Like common cold viruses, EV-D68 mainly causes respiratory infections and is acid-labile. The molecular mechanism by which the acid-sensitive EV-D68 virions uncoat and deliver their genome into a host cell is unknown. Using cryoelectron microscopy (cryo-EM), we have determined the structures of the full native virion and an uncoating intermediate [the A (altered) particle] of EV-D68 at 2.2- and 2.7-Å resolution, respectively. These structures showed that acid treatment of EV-D68 leads to particle expansion, externalization of the viral protein VP1 N termini from the capsid interior, and formation of pores around the icosahedral twofold axes through which the viral RNA can exit. Moreover, because of the low stability of EV-D68, cryo-EM analyses of a mixed population of particles at neutral pH and following acid treatment demonstrated the involvement of multiple structural intermediates during virus uncoating. Among these, a previously undescribed state, the expanded 1 ("E1") particle, shows a majority of internal regions (e.g., the VP1 N termini) to be ordered as in the full native virion. Thus, the E1 particle acts as an intermediate in the transition from full native virions to A particles. Together, the present work delineates the pathway of EV-D68 uncoating and provides the molecular basis for the acid lability of EV-D68 and of the related common cold viruses.
History
DepositionAug 27, 2018-
Header (metadata) releaseSep 5, 2018-
Map releaseDec 19, 2018-
UpdateJan 9, 2019-
Current statusJan 9, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 18.7
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 18.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mzi
  • Surface level: 18.7
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6mzi
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9055.png

Downloads & links

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Map

FileDownload / File: emd_9055.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map in which the inner density is masked out
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.73 Å/pix.
x 264 pix.
= 456.72 Å		1.73 Å/pix.
x 264 pix.
= 456.72 Å		1.73 Å/pix.
x 264 pix.
= 456.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 18.699999999999999 / Movie #1: 18.7
Minimum - Maximum-79.102969999999999 - 114.782679999999999
Average (Standard dev.)0.4190516 (±7.309804)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 456.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.731.731.73
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z456.720456.720456.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-79.103114.7830.419

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Supplemental data

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Half map: unsharpened half map in which the inner density is retained

Fileemd_9055_half_map_1.map
Annotationunsharpened half map in which the inner density is retained
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unsharpened half map in which the inner density is retained

Fileemd_9055_half_map_2.map
Annotationunsharpened half map in which the inner density is retained
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 2
    • Protein or peptide: Viral protein 3
    • 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
Details: Viruses were grown in RD cells and treated with acidic buffer.
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

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Macromolecule #1: Viral protein 1

MacromoleculeName: Viral protein 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18947
SequenceString: IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSN TEP EEAIQTRTVI NQHGVSETLV ENFLSRAALV SKRSFEYKDH TSSTARADKN FFKWTIN TR SFVQLRRKLE LFTYLRFDAE ITILTTVAVN GSGNNTYVGL PDLTLQAMFV PTGALTPE K QDSFHWQSGS ...String:
IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSN TEP EEAIQTRTVI NQHGVSETLV ENFLSRAALV SKRSFEYKDH TSSTARADKN FFKWTIN TR SFVQLRRKLE LFTYLRFDAE ITILTTVAVN GSGNNTYVGL PDLTLQAMFV PTGALTPE K QDSFHWQSGS NASVFFKISD PPARITIPFM CINSAYSVFY DGFAGFEKNG LYGINPADT IGNLCVRIVN EHQPVGFTVT VRVYMKPKHI KAWAPRPPRT LPYMSIANAN YKGKERAPNA LSAIIGNRD SVKTMPHNIV NT

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Macromolecule #2: Viral protein 2

MacromoleculeName: Viral protein 2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18947
SequenceString: SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI D KPTQPETA TDRFYTLKSV KWETGSTGWW WKLPDALNNI GMFGQNVQHH YLYRSGFLIH VQ CNATKFH QGALLVVAIP EHQRGAHNTN TSPGFDDIMK GEEGGTFNHP YVLDDGTSLA CAT ...String:
SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI D KPTQPETA TDRFYTLKSV KWETGSTGWW WKLPDALNNI GMFGQNVQHH YLYRSGFLIH VQ CNATKFH QGALLVVAIP EHQRGAHNTN TSPGFDDIMK GEEGGTFNHP YVLDDGTSLA CAT IFPHQW INLRTNNSAT IVLPWMNAAP MDFPLRHNQW TLAIIPVVPL GTRTTSSMVP ITVS IAPMC CEFNGLRHAI TQ

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Macromolecule #3: Viral protein 3

MacromoleculeName: Viral protein 3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18947
SequenceString: GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNM LEVVQV ESMMEINNTE SAVGMERLKV DISALTDVDQ LLFNIPLDIQ LDGPLRNTLV GNIS RYYTH WSGSLEMTFM FCGSFMAAGK LILCYTPPGG SCPTTRETAM LGTHIVWDFG LQSSV TLII ...String:
GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNM LEVVQV ESMMEINNTE SAVGMERLKV DISALTDVDQ LLFNIPLDIQ LDGPLRNTLV GNIS RYYTH WSGSLEMTFM FCGSFMAAGK LILCYTPPGG SCPTTRETAM LGTHIVWDFG LQSSV TLII PWISGSHYRM FNNDAKSTNA NVGYVTCFMQ TNLIVPSESS DTCSLIGFIA AKDDFS LRL MRDSPDIGQL DHLHAAEAAY Q

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Macromolecule #4: Viral protein 4

MacromoleculeName: Viral protein 4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18947
SequenceString:
GAQVTRQQTG THENANIATN GSHITYNQIN FYKDSYAASA SKQDFSQDPS KFTEPVVEG LKAGAPVLK

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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: 6.5 / Details: phosphate citrate buffer
GridMaterial: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 357 / Average exposure time: 10.5 sec. / Average electron dose: 28.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 39022
CTF correctionSoftware - Name: jspr
Details: On-the-fly CTF correction during 2D alignment and 3D reconstruction
Startup modelType of model: OTHER / Details: Particle orientations were randomly assigned.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 4968
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: jspr
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 0.5 degrees
Software - Name: jspr
Final 3D classificationSoftware - Name: RELION (ver. 2.1.0)
Details: 33863 particles were selected after 2D classification. Subsequently, 3D classification yielded full native virions, A-particles and expanded 1 particles.
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-6mzi:
CryoEM structure of human enterovirus D68 expanded 1 particle (pH 6.5, 4 degrees Celsius, 3 min)

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