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- EMDB-7589: CryoEM structure of human enterovirus D68 A-particle (pH 5.5 and ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7589
TitleCryoEM structure of human enterovirus D68 A-particle (pH 5.5 and 33 degrees Celsius)
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 3
    • Protein or peptide: viral protein 2
  • Ligand: water
Keywordsvirus / genome release / acid
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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : ...: / 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 / cytoplasmic vesicle membrane / : / 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 / host cell nucleus / structural molecule activity / virion attachment to host cell / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus D68 / enterovirus D68
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsLiu Y / Rossmann MG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI011219 United States
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
DepositionMar 19, 2018-
Header (metadata) releaseApr 4, 2018-
Map releaseDec 19, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 21.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 21.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cs4
  • Surface level: 21.5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6cs4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_7589.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map in which the inner density is masked out
Voxel sizeX=Y=Z: 0.65 Å
Density
Contour LevelBy AUTHOR: 21.5 / Movie #1: 21.5
Minimum - Maximum-123.872780000000006 - 178.926819999999992
Average (Standard dev.)0.08302885 (±8.577742000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 467.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.650.650.65
M x/y/z720720720
origin x/y/z0.0000.0000.000
length x/y/z468.000468.000468.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS720720720
D min/max/mean-123.873178.9270.083

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Supplemental data

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

Fileemd_7589_half_map_1.map
Annotationunsharpened half map in which the inner density is retained
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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

Fileemd_7589_half_map_2.map
Annotationunsharpened half map in which the inner density is retained
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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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
  • Ligand: water

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Supramolecule #1: Enterovirus D68

SupramoleculeName: Enterovirus D68 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Viruses were grown in RD cells. / 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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18947
Molecular weightTheoretical: 32.920309 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 KTMPHNIVNT

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 / 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

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 / Strain: US/MO/14-18947
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: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 252 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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: 7.2
Details: Phosphate-citrate buffer. Viruses were treated with phosphate-citrate buffer at pH 5.5 and 33 degrees Celsius, and then neutralized back to about pH 7.2.
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 2-40 / Number grids imaged: 1 / Number real images: 950 / Average exposure time: 8.0 sec. / Average electron dose: 38.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 49098
Startup modelType of model: OTHER / Details: Particle orientations were randomly assigned.
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: jspr
Final 3D classificationSoftware - Name: RELION (ver. 2.0.5)
Details: 23082 full particles were selected after 2D classification.
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 0.5 degrees
Software - Name: jspr
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 23082
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsA combination of the following approaches was used: (1) model rebuilding using Coot, (2) real space refinement using Phenix, (3) reciprocal space refinment using REFMAC5 (as in standard crystallographic refinement).
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-6cs4:
CryoEM structure of human enterovirus D68 A-particle (pH 5.5 and 33 degrees Celsius)

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