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- PDB-4yvs: crystal structure of the virus-like particle of a c4 strain EV71 -

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Basic information

Entry
Database: PDB / ID: 4yvs
Titlecrystal structure of the virus-like particle of a c4 strain EV71
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 / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...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 / 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 / ATP hydrolysis 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 / 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
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)471,74615
Polymers471,74615
Non-polymers00
Water00
1
A: Capsid protein VP1
B: Capsid protein VP3
C: Capsid protein VP0
D: Capsid protein VP1
G: Capsid protein VP1
J: Capsid protein VP1
M: Capsid protein VP1
E: Capsid protein VP3
H: Capsid protein VP3
K: Capsid protein VP3
N: Capsid protein VP3
F: Capsid protein VP0
I: Capsid protein VP0
L: Capsid protein VP0
O: Capsid protein VP0
x 12


Theoretical massNumber of molelcules
Total (without water)5,660,948180
Polymers5,660,948180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area1282620 Å2
ΔGint-7331 kcal/mol
Surface area1221850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)349.746, 349.746, 349.746
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 and segid A
21chain D and segid A
31chain G and segid A
41chain J and segid A
51chain M and segid A
12chain B and segid B
22chain E and segid B
32chain H and segid B
42chain K and segid B
52chain N and segid B
13chain C and segid C
23chain F and segid C
33chain I and segid C
43chain L and segid C
53chain O and segid C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain D and segid AD0
311chain G and segid AG0
411chain J and segid AJ0
511chain M and segid AM0
112chain B and segid BB0
212chain E and segid BE0
312chain H and segid BH0
412chain K and segid BK0
512chain N and segid BN0
113chain C and segid CC0
213chain F and segid CF0
313chain I and segid CI0
413chain L and segid CL0
513chain O and segid CO0

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Capsid protein VP1


Mass: 32699.773 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
#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: 3.78 Å3/Da / Density % sol: 67.45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.1M Imidazole, 1M sodium acetate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. obs: 72397 / % possible obs: 89.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 105.75 Å2 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.101 / Rrim(I) all: 0.163 / Χ2: 1.575 / Net I/av σ(I): 7.25 / Net I/σ(I): 5.7 / Num. measured all: 227650
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.65-3.782.566890.5860.7411.25984
3.78-3.932.569190.6990.5871.27986.40.832
3.93-4.112.670560.8040.4071.38688.40.5840.717
4.11-4.332.771790.8770.2821.48289.60.4130.503
4.33-4.62.973790.9310.1991.71791.60.3020.364
4.6-4.953.374890.9480.1561.901930.2530.299
4.95-5.453.675470.9660.1241.80393.10.2120.247
5.45-6.243.674210.9770.0921.527910.1610.187
6.24-7.853.874180.9910.0551.433900.0990.114
7.85-503.973000.9970.0251.63884.70.0470.054

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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: 3.65→49.964 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3003 1988 2.77 %
Rwork0.2713 69831 -
obs0.2721 71819 88.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 296.42 Å2 / Biso mean: 88.8759 Å2 / Biso min: 41.23 Å2
Refinement stepCycle: final / Resolution: 3.65→49.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26430 0 0 0 26430
Num. residues----3405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00527210
X-RAY DIFFRACTIONf_angle_d1.00137225
X-RAY DIFFRACTIONf_chiral_restr0.0394135
X-RAY DIFFRACTIONf_plane_restr0.0064815
X-RAY DIFFRACTIONf_dihedral_angle_d14.0269705
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5416X-RAY DIFFRACTION7.154TORSIONAL
12D5416X-RAY DIFFRACTION7.154TORSIONAL
13G5416X-RAY DIFFRACTION7.154TORSIONAL
14J5416X-RAY DIFFRACTION7.154TORSIONAL
15M5416X-RAY DIFFRACTION7.154TORSIONAL
21B5205X-RAY DIFFRACTION7.154TORSIONAL
22E5205X-RAY DIFFRACTION7.154TORSIONAL
23H5205X-RAY DIFFRACTION7.154TORSIONAL
24K5205X-RAY DIFFRACTION7.154TORSIONAL
25N5205X-RAY DIFFRACTION7.154TORSIONAL
31C5336X-RAY DIFFRACTION7.154TORSIONAL
32F5336X-RAY DIFFRACTION7.154TORSIONAL
33I5336X-RAY DIFFRACTION7.154TORSIONAL
34L5336X-RAY DIFFRACTION7.154TORSIONAL
35O5336X-RAY DIFFRACTION7.154TORSIONAL
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 (%)
3.6491-3.74040.36151310.34894606473783
3.7404-3.84150.38321350.34664728486385
3.8415-3.95440.4371380.34134766490486
3.9544-4.0820.33051380.32124888502688
4.082-4.22790.28741410.31244898503988
4.2279-4.3970.3121410.28854995513690
4.397-4.5970.32791440.27445092523691
4.597-4.83920.30331480.26335136528492
4.8392-5.14210.27091460.25655176532292
5.1421-5.53870.30591470.25935190533792
5.5387-6.09520.2931450.25695107525290
6.0952-6.97510.28291470.25465147529490
6.9751-8.78010.29261440.2465115525989
8.7801-49.96840.24691430.23514987513082

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