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- PDB-6cv5: CryoEM structure of human enterovirus D68 full particle (after in... -

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Basic information

Entry
Database: PDB / ID: 6cv5
TitleCryoEM structure of human enterovirus D68 full particle (after incubation with low molecular weight heparin)
Components
  • viral protein 1
  • viral protein 2
  • viral protein 3
  • viral protein 4
KeywordsVIRUS / genome release / receptor
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 / nucleoside-triphosphate phosphatase / channel activity ...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 / channel activity / viral capsid / 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
Jelly Rolls - #20 / 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 ...Jelly Rolls - #20 / 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 / Jelly Rolls / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus D68
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsLiu, Y. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Nat Commun / Year: 2019
Title: Bypassing pan-enterovirus host factor PLA2G16.
Authors: Jim Baggen / Yue Liu / Heyrhyoung Lyoo / Arno L W van Vliet / Maryam Wahedi / Jost W de Bruin / Richard W Roberts / Pieter Overduin / Adam Meijer / Michael G Rossmann / Hendrik Jan Thibaut / ...Authors: Jim Baggen / Yue Liu / Heyrhyoung Lyoo / Arno L W van Vliet / Maryam Wahedi / Jost W de Bruin / Richard W Roberts / Pieter Overduin / Adam Meijer / Michael G Rossmann / Hendrik Jan Thibaut / Frank J M van Kuppeveld /
Abstract: Enteroviruses are a major cause of human disease. Adipose-specific phospholipase A2 (PLA2G16) was recently identified as a pan-enterovirus host factor and potential drug target. In this study, we ...Enteroviruses are a major cause of human disease. Adipose-specific phospholipase A2 (PLA2G16) was recently identified as a pan-enterovirus host factor and potential drug target. In this study, we identify a possible mechanism of PLA2G16 evasion by employing a dual glycan receptor-binding enterovirus D68 (EV-D68) strain. We previously showed that this strain does not strictly require the canonical EV-D68 receptor sialic acid. Here, we employ a haploid screen to identify sulfated glycosaminoglycans (sGAGs) as its second glycan receptor. Remarkably, engagement of sGAGs enables this virus to bypass PLA2G16. Using cryo-EM analysis, we reveal that, in contrast to sialic acid, sGAGs stimulate genome release from virions via structural changes that enlarge the putative openings for genome egress. Together, we describe an enterovirus that can bypass PLA2G16 and identify additional virion destabilization as a potential mechanism to circumvent PLA2G16.
History
DepositionMar 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • 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
  • EMDB-7636
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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
D: viral protein 4


Theoretical massNumber of molelcules
Total (without water)95,0614
Polymers95,0614
Non-polymers00
Water2,828157
1
A: viral protein 1
B: viral protein 3
C: viral protein 2
D: viral protein 4
x 60


Theoretical massNumber of molelcules
Total (without water)5,703,631240
Polymers5,703,631240
Non-polymers00
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: viral protein 1
B: viral protein 3
C: viral protein 2
D: viral protein 4
x 5


  • icosahedral pentamer
  • 475 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)475,30320
Polymers475,30320
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: viral protein 1
B: viral protein 3
C: viral protein 2
D: viral protein 4
x 6


  • icosahedral 23 hexamer
  • 570 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)570,36324
Polymers570,36324
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein viral protein 1


Mass: 32957.449 Da / Num. of mol.: 1 / Fragment: UNP residues 565-861 / Source method: isolated from a natural source / Source: (natural) Enterovirus D68 / Cell line: rhabdomyosarcoma / Strain: 947 / References: UniProt: A0A0X7Z9B1
#2: Protein viral protein 3


Mass: 27170.895 Da / Num. of mol.: 1 / Fragment: UNP residues 1-247 / Source method: isolated from a natural source / Source: (natural) Enterovirus D68 / Cell line: rhabdomyosarcoma / Strain: 947 / References: UniProt: E9RIT6
#3: Protein viral protein 2


Mass: 27595.215 Da / Num. of mol.: 1 / Fragment: UNP residues 1-248 / Source method: isolated from a natural source / Source: (natural) Enterovirus D68 / Cell line: rhabdomyosarcoma / Strain: 947 / References: UniProt: A0A097ZN88, UniProt: A0A0X7Z9B1*PLUS
#4: Protein viral protein 4


Mass: 7336.960 Da / Num. of mol.: 1 / Fragment: UNP residues 2-69 / Source method: isolated from a natural source / Source: (natural) Enterovirus D68 / Cell line: rhabdomyosarcoma / Strain: 947 / References: UniProt: A0A0P0DH17
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY / Number of used crystals: 1
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Enterovirus D68 / Type: VIRUS / Details: Grown in RD cells / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Enterovirus D68 / Strain: 947
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.2 / Details: phosphate buffer
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Homemade
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated defocus min: 600 nm / Calibrated defocus max: 4500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7 sec. / Electron dose: 33 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 872
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 35 / Used frames/image: 2-35

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
REFMACrefinement
PDB_EXTRACT3.22data extraction
EM software
IDNameVersionCategoryDetails
1EMAN2particle selectione2boxer.py
2Leginon3.2image acquisition
4CTFFIND4.1CTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10jsprinitial Euler assignment
11jsprfinal Euler assignment
12RELION2.0.5classification
13jspr3D reconstruction
14PHENIXmodel refinement
15REFMACmodel refinement
16Cootmodel refinement
CTF correctionDetails: On-the-fly CTF correction during 2D alignment and 3D reconstruction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 18049
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5104 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient
Displacement parametersBiso max: 152.93 Å2 / Biso mean: 26.5606 Å2 / Biso min: 2 Å2

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