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- PDB-4rs5: Crystal structure of an uncoating intermediate of a EV71 recombin... -

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Basic information

Entry
Database: PDB / ID: 4rs5
TitleCrystal structure of an uncoating intermediate of a EV71 recombinant virus
Components
  • Capsid protein VP0
  • Capsid protein VP1
  • Capsid protein VP3
KeywordsVIRUS / eight-stranded beta barrel / replicate in cytoplasm
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: 3.805 Å
AuthorsChen, R. / Lyu, K.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal structures of enterovirus 71 (EV71) recombinant virus particles provide insights into vaccine design.
Authors: Lyu, K. / Wang, G.C. / He, Y.L. / Han, J.F. / Ye, Q. / Qin, C.F. / Chen, R.
History
DepositionNov 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)480,09615
Polymers480,09615
Non-polymers00
Water00
1
E: Capsid protein VP3
F: Capsid protein VP0
D: Capsid protein VP1
M: Capsid protein VP1
A: Capsid protein VP1
G: Capsid protein VP1
J: Capsid protein VP1
N: Capsid protein VP3
B: Capsid protein VP3
H: Capsid protein VP3
K: Capsid protein VP3
O: Capsid protein VP0
C: Capsid protein VP0
I: Capsid protein VP0
L: Capsid protein VP0
x 12


Theoretical massNumber of molelcules
Total (without water)5,761,147180
Polymers5,761,147180
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 area1252720 Å2
ΔGint-6897 kcal/mol
Surface area1295310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)350.155, 350.155, 350.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
DetailsThe biological assembly is a 60mer generated from the pentamer in the asymmetric unit by the following 12 operations: (x,y,z),(-x,-y,z),(-x,y,-z),(x,-y,-z),(y,z,x),(-y,-z,x),(-y,z,-x),(y,-z,-x),(z,x,y),(-z,-x,y),(-z,x,-y) and (z,-x,-y). The pentamer in the asymmetric unit is generated from the deposited PDB by the following transformations(r11,r12,r13,r21,r22,r23,r31,r32,r33,tx,tx,tz):(1,0,0,0,1,0,0,0,1,0,0,0), (-0.8127, 0.5018, -0.2962, -0.4896, -0.3124, 0.8141, 0.316, 0.8066, 0.4996, 1.955, 0.5457, -0.138), (0.3088, 0.809, -0.5002, -0.8085, 0.5003, 0.3099, 0.501, 0.3087, 0.8086, -0.07626, 0.23, -0.006095), (-0.8092, -0.4849, 0.3318, 0.5077, -0.2928, 0.8103, -0.2957, 0.8241, 0.4831, 4.346, 1.46, -1.11) and (0.2998, -0.8038, 0.5138, 0.803, 0.5034, 0.319, -0.515, 0.3169, 0.7964, 2.491, 1.66, -0.7237).

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Components

#1: 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 / Cell line (production host): RD cells / Production host: Homo sapiens (human) / References: UniProt: F6KTB0
#2: 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 / Cell line (production host): RD cells / Production host: Homo sapiens (human) / References: UniProt: F6KTB0
#3: Protein
Capsid protein VP1


Mass: 34369.754 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Cell line (production host): RD cells / Production host: Homo sapiens (human) / 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: 3.73 Å3/Da / Density % sol: 66.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M MES containing 1.6M sodium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.281579 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2013
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.281579 Å / Relative weight: 1
ReflectionResolution: 3.805→46.791 Å / Num. all: 119163 / Num. obs: 97564 / % possible obs: 81.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.8→3.94 Å / % possible all: 94

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.805→46.791 Å / σ(F): 1.34 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2994 1998 random
Rwork0.2705 --
all0.2714 66735 -
obs0.2714 66626 -
Refinement stepCycle: LAST / Resolution: 3.805→46.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26425 0 0 0 26425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.005
X-RAY DIFFRACTIONf_bond_d0.981
X-RAY DIFFRACTIONf_dihedral_angle_d13.167
LS refinement shellResolution: 3.8→3.9 Å
RfactorNum. reflection% reflection
Rfree0.3929 142 -
Rwork0.367 --
obs-4573 93 %

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