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- PDB-6csa: CryoEM structure of human enterovirus D68 emptied particle (pH 5.... -

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Basic information

Entry
Database: PDB / ID: 6csa
TitleCryoEM structure of human enterovirus D68 emptied particle (pH 5.5 and room temperature)
Components
  • viral protein 1
  • viral protein 2
  • viral protein 3
KeywordsVIRUS / virus / genome release / acid
Function / homologyPeptidase C3A/C3B, picornaviral / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid ...Peptidase C3A/C3B, picornaviral / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / 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/Calicivirus coat protein / Viral coat protein subunit / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / RNA helicase / picornavirus capsid protein / 3C cysteine protease (picornain 3C) / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / Picornavirus 2B protein / RNA dependent RNA polymerase / Picornavirus core protein 2A / 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 / T=pseudo3 icosahedral viral capsid / 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 / RNA-directed RNA polymerase / induction by virus of host autophagy / suppression by virus of host gene expression / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein / Genome polyprotein
Function and homology information
Specimen sourceEnterovirus D68
enterovirus D68
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.75 Å resolution
AuthorsLiu, Y. / Rossmann, M.G.
Funding supportUnited States , 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteAI011219United 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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 20, 2018 / Release: Dec 19, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 19, 2018Structure modelrepositoryInitial release
1.1Dec 26, 2018Structure modelData collection / Database referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Jan 9, 2019Structure modelData collection / Database referencescitation / citation_author_citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: viral protein 1
B: viral protein 3
C: viral protein 2


Theoretical massNumber of molelcules
Total (without water)87,6003
Polyers87,6003
Non-polymers00
Water0
1
A: viral protein 1
B: viral protein 3
C: viral protein 2
x 60


Theoretical massNumber of molelcules
Total (without water)5,256,015180
Polyers5,256,015180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: viral protein 1
B: viral protein 3
C: viral protein 2
x 5


  • icosahedral pentamer
  • 438 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)438,00115
Polyers438,00115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: viral protein 1
B: viral protein 3
C: viral protein 2
x 6


  • icosahedral 23 hexamer
  • 526 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)525,60218
Polyers525,60218
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein/peptide viral protein 1 /


Mass: 32920.309 Da / Num. of mol.: 1 / Fragment: UNP residues 565-861 / Source: (natural) Enterovirus D68 / Cell line: rhabdomyosarcoma / Strain: US/MO/14-18947 / References: UniProt: A0A097BW12
#2: Protein/peptide viral protein 3 /


Mass: 27112.814 Da / Num. of mol.: 1 / Fragment: UNP residues 318-564 / Source: (natural) enterovirus D68 / Cell line: rhabdomyosarcoma / Strain: US/MO/14-18947 / References: UniProt: A0A097BW12
#3: Protein/peptide viral protein 2 /


Mass: 27567.135 Da / Num. of mol.: 1 / Fragment: UNP residues 70-317 / Source: (natural) enterovirus D68 / Cell line: rhabdomyosarcoma / Strain: US/MO/14-18947 / References: UniProt: A0A1I9KXX3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY / Number of used crystals: 1
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Enterovirus D68Enterovirus 68 / Type: VIRUS / Details: Viruses were grown in RD cells. / Entity ID: 1, 2, 3 / Source: NATURAL
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18947
Details of virusEmpty: YES / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRION
Buffer solutionDetails: Phosphate-citrate buffer. Viruses were treated with phosphate-citrate buffer at pH 5.5 and room temperature Celsius, and then neutralized back to about pH 7.2.
pH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Homemade
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 298 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 / Nominal defocus max: 4800 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 28 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 144
Image scansSampling size: 5 microns / Width: 3710 / Height: 3838 / Movie frames/image: 30 / Used frames/image: 3-16

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Processing

Software
NameVersionClassificationContact authorContact author emailLanguageLocationTypeDate
PHENIXrefinementPaul D. AdamsPDAdams[at]lbl.govC++http://www.phenix-online.org/package
REFMACrefinementGarib N. Murshudovgarib[at]ysbl.york.ac.ukFortran_77http://www.ccp4.ac.uk/dist/html/refmac5.htmlprogram
PDB_EXTRACT3.22data extractionPDBdeposit[at]deposit.rcsb.orgC++http://sw-tools.pdb.org/apps/PDB_EXTRACT/packageJuly. 13, 2016
EM software
IDNameVersionCategory
1EMAN2particle selection
2Leginon3.2image acquisition
4jsprCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
11Cootmodel refinement
12REFMACmodel refinement
13jsprinitial Euler assignment
14jsprfinal Euler assignment
15RELION2.0.5classification
16jspr3D reconstruction
CTF correctionDetails: On-the-fly CTF correction during 2D alignment and 3D reconstruction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 6578
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 2150 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingDetails: A 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).
Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Correlation coefficient
Displacement parametersB iso max: 336.99 Å2 / B iso mean: 49.1735 Å2 / B iso min: 3.8 Å2

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