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- PDB-5tsk: Molecular Dynamics Flexible Fitting Model of Coxsackievirus A16 e... -

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Basic information

Entry
Database: PDB / ID: 5tsk
TitleMolecular Dynamics Flexible Fitting Model of Coxsackievirus A16 empty Procapsid VP1 Subunit
Componentscoxsackievirus A16 empty procapsid VP1 subunit
KeywordsVIRUS / coxsackievirus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 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 / monoatomic ion transmembrane transport / RNA helicase activity / induction by virus of host autophagy / 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
Similarity search - Function
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) ...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
Biological speciesCoxsackievirus A16
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsFan, C. / Cong, Y. / Ye, X. / Huang, Z.
CitationJournal: J Virol / Year: 2017
Title: Beta-Propiolactone Inactivation of Coxsackievirus A16 Induces Structural Alteration and Surface Modification of Viral Capsids.
Authors: Chen Fan / Xiaohua Ye / Zhiqiang Ku / Liangliang Kong / Qingwei Liu / Cong Xu / Yao Cong / Zhong Huang /
Abstract: Beta-propiolactone (BPL) is an inactivating agent that is widely used in the vaccine industry. However, its effects on vaccine protein antigens and its mechanisms of action remain poorly understood. ...Beta-propiolactone (BPL) is an inactivating agent that is widely used in the vaccine industry. However, its effects on vaccine protein antigens and its mechanisms of action remain poorly understood. Here we present cryo-electron microscopy (cryo-EM) structures of BPL-treated coxsackievirus A16 (CVA16) mature virions and procapsids at resolutions of 3.9 Å and 6.5 Å, respectively. Notably, both particles were found to adopt an expanded conformation resembling the 135S-like uncoating intermediate, with characteristic features including an opened 2-fold channel, the externalization of the N terminus of VP1 capsid protein, and the absence of pocket factor. However, major neutralizing epitopes are very well preserved on these particles. Further biochemical analyses revealed that BPL treatment impairs the abilities of CVA16 particles to bind to the attachment receptor heparan sulfate and to a conformation-dependent monoclonal antibody in a BPL dose-dependent manner, indicating that BPL is able to modify surface-exposed amino acid residues. Taken together, our results demonstrate that BPL treatment may induce alteration of the overall structure and surface properties of a nonenveloped viral capsid, thus revealing a novel mode of action of BPL. Beta-propiolactone (BPL) is commonly used as an inactivating reagent to produce viral vaccines. It is recognized that BPL inactivates viral infectivity through modification of viral nucleic acids. However, its effect on viral proteins remains largely unknown. Here, we present high-resolution cryo-EM structures of BPL-treated coxsackievirus A16 (CVA16) mature virions and procapsids, which reveals an expanded overall conformation and characteristic features that are typical for the 135S-like uncoating intermediate. We further show that the BPL concentration affects the binding of inactivated CVA16 particles to their receptor/antibody. Thus, BPL treatment can alter the overall structure and surface properties of viral capsids, which may lead to antigenic and immunogenic variations. Our findings provide important information for future development of BPL-inactivated vaccines.
History
DepositionOct 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Other / Category: atom_sites / cell / em_image_scans
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.2Dec 11, 2019Group: Experimental preparation / Category: em_sample_support / Item: _em_sample_support.grid_type
Revision 1.3Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _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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Assembly

Deposited unit
A: coxsackievirus A16 empty procapsid VP1 subunit


Theoretical massNumber of molelcules
Total (without water)33,0901
Polymers33,0901
Non-polymers00
Water00
1
A: coxsackievirus A16 empty procapsid VP1 subunit
x 60


Theoretical massNumber of molelcules
Total (without water)1,985,42160
Polymers1,985,42160
Non-polymers00
Water0
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: coxsackievirus A16 empty procapsid VP1 subunit
x 5


  • icosahedral pentamer
  • 165 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)165,4525
Polymers165,4525
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: coxsackievirus A16 empty procapsid VP1 subunit
x 6


  • icosahedral 23 hexamer
  • 199 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)198,5426
Polymers198,5426
Non-polymers00
Water0
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
6
A: coxsackievirus A16 empty procapsid VP1 subunit
x 60


  • crystal asymmetric unit, crystal frame
  • 1.99 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,985,42160
Polymers1,985,42160
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.309017, -0.5, -0.80901699), (0.5, 0.80901699, -0.309017), (0.80901699, -0.309017, 0.5)
3generate(-0.80901699, -0.309017, -0.5), (0.30901699, 0.5, -0.809017), (0.5, -0.809017, -0.309017)
4generate(-0.809017, 0.309017, 0.5), (-0.309017, 0.5, -0.80901699), (-0.5, -0.809017, -0.30901699)
5generate(0.30901699, 0.5, 0.809017), (-0.5, 0.809017, -0.30901699), (-0.80901699, -0.30901699, 0.5)
6generate(-0.5, -0.80901699, 0.30901699), (-0.809017, 0.30901699, -0.49999999), (0.309017, -0.50000001, -0.80901699)
7generate(-0.309017, -0.5, 0.80901699), (-0.5, 0.80901699, 0.309017), (-0.80901699, -0.309017, -0.5)
8generate(0.30901699, -0.5, 0.80901699), (0.5, 0.80901699, 0.309017), (-0.809017, 0.30901699, 0.5)
9generate(0.5, -0.80901699, 0.30901699), (0.809017, 0.30901699, -0.5), (0.30901699, 0.5, 0.809017)
10generate(-1), (-1), (1)
11generate(0.30901699, 0.49999999, -0.809017), (0.50000001, -0.80901699, -0.309017), (-0.80901699, -0.30901699, -0.5)
12generate(-0.309017, 0.5, -0.80901699), (-0.5, -0.80901699, -0.309017), (-0.80901699, 0.309017, 0.5)
13generate(-0.5, 0.809017, -0.30901699), (-0.809017, -0.30901699, 0.5), (0.30901699, 0.5, 0.80901699)
14generate(1), (1), (1)
15generate(0.5, 0.80901699, -0.309017), (0.809017, -0.30901699, 0.5), (0.309017, -0.5, -0.809017)
16generate(-0.80901699, 0.309017, 0.50000001), (0.30901699, -0.5, 0.80901699), (0.49999999, 0.809017, 0.30901699)
17generate(0.309017, 0.5, 0.80901699), (0.5, -0.80901699, 0.309017), (0.80901699, 0.309017, -0.5)
18generate(1), (-1), (-1)
19generate(0.30901699, -0.5, -0.809017), (-0.5, -0.80901699, 0.30901699), (-0.80901699, 0.309017, -0.5)
20generate(-0.80901699, -0.30901699, -0.5), (-0.309017, -0.5, 0.80901699), (-0.5, 0.809017, 0.30901699)
21generate(-0.49999999, -0.809017, -0.30901699), (0.80901699, -0.309017, -0.50000001), (0.30901699, -0.5, 0.80901699)
22generate(-0.80901699, -0.309017, 0.5), (-0.309017, -0.5, -0.80901699), (0.5, -0.80901699, 0.309017)
23generate(1), (-1), (-1)
24generate(0.80901699, -0.309017, 0.5), (-0.30901699, 0.5, 0.809017), (-0.5, -0.80901699, 0.30901699)
25generate(0.5, -0.809017, -0.30901699), (0.80901699, 0.30901699, 0.5), (-0.309017, -0.5, 0.80901699)
26generate(0.80901699, 0.30901699, 0.5), (-0.30901699, -0.49999999, 0.809017), (0.50000001, -0.80901699, -0.309017)
27generate(0.80901699, -0.309017, -0.5), (0.309017, -0.5, 0.80901699), (-0.5, -0.80901699, -0.309017)
28generate(-0.30901699, -0.5, -0.80901699), (0.5, -0.809017, 0.30901699), (-0.809017, -0.30901699, 0.5)
29generate(-1), (-1), (1)
30generate(-0.309017, 0.5, 0.809017), (-0.5, -0.80901699, 0.309017), (0.809017, -0.30901699, 0.5)
31generate(-0.309017, 0.50000001, 0.80901699), (0.5, 0.80901699, -0.30901699), (-0.809017, 0.30901699, -0.49999999)
32generate(0.80901699, 0.309017, 0.5), (0.309017, 0.5, -0.80901699), (-0.5, 0.80901699, 0.309017)
33generate(0.809017, -0.30901699, -0.5), (-0.30901699, 0.5, -0.80901699), (0.5, 0.80901699, 0.309017)
34generate(-0.30901699, -0.5, -0.809017), (-0.5, 0.80901699, -0.30901699), (0.809017, 0.30901699, -0.5)
35generate(-1), (1), (-1)
36generate(-1), (-1), (1)
37generate(-0.80901699, 0.309017, -0.5), (-0.309017, 0.5, 0.80901699), (0.5, 0.80901699, -0.309017)
38generate(-0.5, 0.809017, 0.309017), (0.80901699, 0.309017, 0.5), (0.30901699, 0.5, -0.809017)
39generate(0.5, 0.809017, 0.30901699), (0.809017, -0.309017, -0.5), (-0.309017, 0.5, -0.80901699)
40generate(0.80901699, 0.30901699, -0.5), (-0.30901699, -0.5, -0.809017), (-0.5, 0.809017, -0.30901699)
41generate(-0.50000001, 0.80901699, 0.309017), (-0.80901699, -0.30901699, -0.5), (-0.30901699, -0.49999999, 0.809017)
42generate(0.5, 0.80901699, 0.309017), (-0.80901699, 0.309017, 0.5), (0.309017, -0.5, 0.80901699)
43generate(0.809017, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699), (0.5, -0.809017, 0.30901699)
44generate(-1), (1), (-1)
45generate(-0.809017, 0.30901699, -0.5), (0.309017, -0.5, -0.809017), (-0.5, -0.80901699, 0.309017)
46generate(-0.30901699, 0.5, -0.80901699), (0.49999999, 0.809017, 0.30901699), (0.80901699, -0.309017, -0.50000001)
47generate(-0.5, 0.80901699, -0.309017), (0.80901699, 0.309017, -0.5), (-0.309017, -0.5, -0.80901699)
48generate(1), (-1), (-1)
49generate(0.5, 0.80901699, -0.30901699), (-0.80901699, 0.309017, -0.5), (-0.30901699, 0.5, 0.809017)
50generate(0.309017, 0.5, -0.80901699), (-0.5, 0.809017, 0.30901699), (0.80901699, 0.30901699, 0.5)
51generate(-1), (1), (-1)
52generate(-0.5, -0.80901699, 0.309017), (0.80901699, -0.309017, 0.5), (-0.309017, 0.5, 0.80901699)
53generate(-0.30901699, -0.5, 0.809017), (0.5, -0.809017, -0.309017), (0.80901699, 0.309017, 0.5)
54generate(0.309017, -0.5, 0.80901699), (-0.5, -0.809017, -0.30901699), (0.809017, -0.309017, -0.5)
55generate(0.5, -0.809017, 0.30901699), (-0.80901699, -0.30901699, 0.5), (-0.30901699, -0.5, -0.809017)
56generate(0.809017, -0.30901699, 0.49999999), (0.309017, -0.50000001, -0.80901699), (0.5, 0.80901699, -0.30901699)
57generate(0.5, -0.80901699, -0.309017), (-0.80901699, -0.309017, -0.5), (0.309017, 0.5, -0.80901699)
58generate(-0.5, -0.80901699, -0.309017), (-0.809017, 0.30901699, 0.5), (-0.30901699, 0.5, -0.80901699)
59generate(-0.809017, -0.30901699, 0.5), (0.30901699, 0.5, 0.809017), (-0.5, 0.80901699, -0.30901699)
60generate(1), (1), (1)

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Components

#1: Protein coxsackievirus A16 empty procapsid VP1 subunit


Mass: 33090.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxsackievirus A16 / Cell line: Vero / Strain: SZ05 / References: UniProt: A9LXZ4*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: coxsackievirus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Coxsackievirus A16
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.6 / Details: 0.15 M phosphate buffered saline(PBS) buffer
Buffer componentConc.: 0.15 M / Name: phosphate buffered saline / Formula: phosphate
SpecimenConc.: 3.22 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 120 K / Details: Blot for 2 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Details: Objective lens astigmatism was corrected at 75000 magnification
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 57000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm / Cs: 0.005 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 90 K / Temperature (min): 70 K
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1jsprparticle selection
4jsprCTF correction
7NAMD2.1model fitting
9jsprinitial Euler assignment
10jsprfinal Euler assignment
11jsprclassification
12jspr3D reconstruction
13NAMD2.1model refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1642 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Weighting factor of 0.5 was chosen to weigh the contribution of the cryo-EM map in the molecular dynamic simulation. The simulation started with 20 000 steps of minimization followed by 100 ...Details: Weighting factor of 0.5 was chosen to weigh the contribution of the cryo-EM map in the molecular dynamic simulation. The simulation started with 20 000 steps of minimization followed by 100 000 steps of molecular dynamics before converging.
Atomic model buildingPDB-ID: 4JGY

4jgy


Pdb chain-ID: A / Accession code: 4JGY / Pdb chain residue range: 74-297 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 6.5 Å

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