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- PDB-4yvw: crystal structure of an enterovirus 71/coxsackievirus A16 chimeri... -

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Basic information

Entry
Database: PDB / ID: 4yvw
Titlecrystal structure of an enterovirus 71/coxsackievirus A16 chimeric virus-like particle
Components
  • Capsid protein VP0
  • Capsid protein VP1
  • Capsid protein VP3
KeywordsVIRUS / virus-like particle / neutralization epitope
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 / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...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 / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Jelly Rolls - #20 / 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 ...Jelly Rolls - #20 / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsChen, R. / Lyu, K.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370730 China
National Natural Science Foundation of China31070144 China
Ministry of Science and Technology of China2010CB912403 China
CitationJournal: J.Virol. / Year: 2015
Title: Crystal Structures of Yeast-Produced Enterovirus 71 and Enterovirus 71/Coxsackievirus A16 Chimeric Virus-Like Particles Provide the Structural Basis for Novel Vaccine Design against Hand-Foot-and-Mouth Disease
Authors: Lyu, K. / He, Y.L. / Li, H.Y. / Chen, R.
History
DepositionMar 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Capsid protein VP1
F: Capsid protein VP3
G: Capsid protein VP0
A: Capsid protein VP1
D: Capsid protein VP1
J: Capsid protein VP1
M: Capsid protein VP1
B: Capsid protein VP3
H: Capsid protein VP3
K: Capsid protein VP3
N: Capsid protein VP3
C: Capsid protein VP0
I: Capsid protein VP0
L: Capsid protein VP0
O: Capsid protein VP0


Theoretical massNumber of molelcules
Total (without water)471,23015
Polymers471,23015
Non-polymers00
Water00
1
E: Capsid protein VP1
F: Capsid protein VP3
G: Capsid protein VP0
A: Capsid protein VP1
D: Capsid protein VP1
J: Capsid protein VP1
M: Capsid protein VP1
B: Capsid protein VP3
H: Capsid protein VP3
K: Capsid protein VP3
N: Capsid protein VP3
C: Capsid protein VP0
I: Capsid protein VP0
L: Capsid protein VP0
O: Capsid protein VP0
x 12


Theoretical massNumber of molelcules
Total (without water)5,654,759180
Polymers5,654,759180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_955-x+4,-y,z1
crystal symmetry operation3_957-x+4,y,-z+21
crystal symmetry operation4_557x,-y,-z+21
crystal symmetry operation5_636z+1,x-2,y+11
crystal symmetry operation6_676z+1,-x+2,-y+11
crystal symmetry operation7_876-z+3,-x+2,y+11
crystal symmetry operation8_836-z+3,x-2,-y+11
crystal symmetry operation9_744y+2,z-1,x-11
crystal symmetry operation10_748-y+2,z-1,-x+31
crystal symmetry operation11_768y+2,-z+1,-x+31
crystal symmetry operation12_764-y+2,-z+1,x-11
Buried area1247260 Å2
ΔGint-7013 kcal/mol
Surface area1304890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)349.151, 349.151, 349.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number208
Space group name H-MP4232
SymmetryPoint symmetry: (Schoenflies symbol: C (n fold cyclic))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D
31chain E
41chain J
51chain M
12chain B
22chain F
32chain H
42chain K
52chain N
13chain C
23chain G
33chain I
43chain L
53chain O

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTHRTHRchain AAD72 - 29672 - 296
21SERSERTHRTHRchain DDE72 - 29672 - 296
31SERSERTHRTHRchain EEA72 - 29672 - 296
41SERSERTHRTHRchain JJF72 - 29672 - 296
51SERSERTHRTHRchain MMG72 - 29672 - 296
12GLYGLYLEULEUchain BBH1 - 2361 - 236
22GLYGLYLEULEUchain FFB1 - 2361 - 236
32GLYGLYLEULEUchain HHI1 - 2361 - 236
42GLYGLYLEULEUchain KKJ1 - 2361 - 236
52GLYGLYLEULEUchain NNK1 - 2361 - 236
13LEULEUGLNGLNchain CCL16 - 25085 - 319
23LEULEUGLNGLNchain GGC16 - 25085 - 319
33LEULEUGLNGLNchain IIM16 - 25085 - 319
43LEULEUGLNGLNchain LLN16 - 25085 - 319
53LEULEUGLNGLNchain OOO16 - 25085 - 319

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Capsid protein VP1


Mass: 32596.613 Da / Num. of mol.: 5 / Mutation: K215L, E217A, K218N, E221D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: F6KTB0
#2: Protein
Capsid protein VP3


Mass: 26440.148 Da / Num. of mol.: 5 / Mutation: K550Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: F6KTB0
#3: Protein
Capsid protein VP0


Mass: 35209.219 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: F6KTB0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.76 Å3/Da / Density % sol: 67.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 0.5M Magnesium formate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.281579 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.281579 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 56842 / % possible obs: 79.2 % / Redundancy: 2.2 % / Biso Wilson estimate: 122.54 Å2 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.13 / Rrim(I) all: 0.204 / Χ2: 1.48 / Net I/av σ(I): 4.607 / Net I/σ(I): 4.1 / Num. measured all: 123302
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Χ2% possible allRmerge(I) obsRpim(I) allRrim(I) all
3.8-3.871.825960.3741.26174.4
3.87-3.941.826560.441.22675.3
3.94-4.011.826760.4751.22875.7
4.01-4.091.826910.5321.29576.30.9950.816
4.09-4.181.927250.6641.2677.30.7950.64
4.18-4.281.927370.6751.31977.60.7550.6050.974
4.28-4.391.928120.7621.39479.10.5690.4570.734
4.39-4.5228430.8151.41980.40.4940.390.634
4.5-4.64228700.8341.45980.90.4340.3390.554
4.64-4.792.129510.8651.39482.50.3940.2950.495
4.79-4.962.229520.8961.45683.30.3420.2520.428
4.96-5.162.329770.9051.41183.60.3010.220.375
5.16-5.392.330120.9121.416840.3080.2210.382
5.39-5.672.429340.9251.42820.2730.1940.337
5.67-6.032.429080.9321.32480.50.2420.1690.297
6.03-6.492.429310.9481.39381.40.2050.1470.254
6.49-7.152.529420.971.485810.1610.1120.197
7.15-8.182.529190.9831.56179.80.1120.0770.137
8.18-10.292.529010.9941.84177.90.0650.0440.08
10.29-502.628090.9922.26771.60.0560.0380.068

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(phenix.refine: dev_1839)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1POV

1pov


Resolution: 3.8→47.96 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3243 1988 3.52 %
Rwork0.2863 54426 -
obs0.2876 56414 78.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 233.09 Å2 / Biso mean: 112.7409 Å2 / Biso min: 66.45 Å2
Refinement stepCycle: final / Resolution: 3.8→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26525 0 0 0 26525
Num. residues----3420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00527310
X-RAY DIFFRACTIONf_angle_d1.12337380
X-RAY DIFFRACTIONf_chiral_restr0.0444165
X-RAY DIFFRACTIONf_plane_restr0.0064830
X-RAY DIFFRACTIONf_dihedral_angle_d14.1229705
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5383X-RAY DIFFRACTION9.398TORSIONAL
12D5383X-RAY DIFFRACTION9.398TORSIONAL
13E5383X-RAY DIFFRACTION9.398TORSIONAL
14J5383X-RAY DIFFRACTION9.398TORSIONAL
15M5383X-RAY DIFFRACTION9.398TORSIONAL
21B5230X-RAY DIFFRACTION9.398TORSIONAL
22F5230X-RAY DIFFRACTION9.398TORSIONAL
23H5230X-RAY DIFFRACTION9.398TORSIONAL
24K5230X-RAY DIFFRACTION9.398TORSIONAL
25N5230X-RAY DIFFRACTION9.398TORSIONAL
31C5390X-RAY DIFFRACTION9.398TORSIONAL
32G5390X-RAY DIFFRACTION9.398TORSIONAL
33I5390X-RAY DIFFRACTION9.398TORSIONAL
34L5390X-RAY DIFFRACTION9.398TORSIONAL
35O5390X-RAY DIFFRACTION9.398TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.7985-3.89340.4411290.37183462359172
3.8934-3.99870.37041310.36393563369473
3.9987-4.11630.40241340.34563678381276
4.1163-4.2490.3841370.34323741387877
4.249-4.40080.34931400.32243841398179
4.4008-4.57690.33841440.31283945408981
4.5769-4.7850.3171470.29194026417382
4.785-5.0370.36721490.28274078422783
5.037-5.35220.32291500.28174114426484
5.3522-5.76480.34851480.2964041418982
5.7648-6.34380.30971460.27684004415081
6.3438-7.2590.31971470.29084053420081
7.259-9.13530.2931450.26434009415479
9.1353-47.96340.25391410.2233871401273

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