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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: 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
SampleEnterovirus D68Enterovirus 68:
virus / (Viral protein ...) x 4
Function / homologyPeptidase C3, picornavirus core protein 2A / Picornavirus coat protein VP4 superfamily / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus ...Peptidase C3, picornavirus core protein 2A / Picornavirus coat protein VP4 superfamily / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / P-loop containing nucleoside triphosphate hydrolase / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Poliovirus 3A protein-like / Poliovirus core protein 3a, soluble domain / Helicase, superfamily 3, single-stranded RNA virus / Picornavirus coat protein (VP4) / picornavirus capsid protein / 3C cysteine protease (picornain 3C) / RNA dependent RNA polymerase / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / RNA helicase / Poliovirus 3A protein like / Picornavirus core protein 2A / Picornavirus 2B protein / T=pseudo3 icosahedral viral capsid / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / viral capsid / RNA-directed RNA polymerase / suppression by virus of host gene expression / induction by virus of host autophagy / ion channel activity / protein complex oligomerization / peptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / virion attachment to host cell / viral process / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein / Polyprotein / Polyprotein
Function and homology information
SourceEnterovirus D68
Methodsingle particle reconstruction / cryo EM / 3.46 Å resolution
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
Validation ReportPDB-ID: 6mzi

SummaryFull reportAbout validation report
DateDeposition: Aug 27, 2018 / Header (metadata) release: Sep 5, 2018 / Map release: Dec 19, 2018 / Last update: Jan 9, 2019

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Structure visualization

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

Downloads & links

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Map

Fileemd_9055.map.gz (map file in CCP4 format, 73600 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
264 pix
1.73 Å/pix.
= 456.72 Å
264 pix
1.73 Å/pix.
= 456.72 Å
264 pix
1.73 Å/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
Contour Level:18.7 (by author), 18.7 (movie #1):
Minimum - Maximum-79.102969999999999 - 114.782679999999999
Average (Standard dev.)0.4190516 (7.309804)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions264264264
Origin0.00.00.0
Limit263.0263.0263.0
Spacing264264264
CellA=B=C: 456.72 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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Sample components

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Entire Enterovirus D68

EntireName: Enterovirus D68
Details: Viruses were grown in RD cells and treated with acidic buffer.
Number of components: 5

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Component #1: virus, Enterovirus D68

VirusName: Enterovirus D68Enterovirus 68 / Class: VIRION
Details: Viruses were grown in RD cells and treated with acidic buffer.
Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Enterovirus D68 / Strain: US/MO/14-18947

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Component #2: protein, Viral protein 1

ProteinName: Viral protein 1 / Recombinant expression: No
SourceSpecies: Enterovirus D68 / Strain: US/MO/14-18947

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Component #3: protein, Viral protein 2

ProteinName: Viral protein 2 / Recombinant expression: No
SourceSpecies: Enterovirus D68 / Strain: US/MO/14-18947

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Component #4: protein, Viral protein 3

ProteinName: Viral protein 3 / Recombinant expression: No
SourceSpecies: Enterovirus D68 / Strain: US/MO/14-18947

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Component #5: protein, Viral protein 4

ProteinName: Viral protein 4 / Recombinant expression: No
SourceSpecies: Enterovirus D68 / Strain: US/MO/14-18947

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: phosphate citrate buffer / pH: 6.5
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 28 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 8500.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 357 / Sampling size: 5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 4968
3D reconstructionAlgorithm: FOURIER SPACE / Software: jspr
CTF correction: On-the-fly CTF correction during 2D alignment and 3D reconstruction
Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
Output model

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