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- PDB-4rqp: Crystal structure of the natually occurring empty particle of a c... -

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Basic information

Entry
Database: PDB / ID: 4rqp
TitleCrystal structure of the natually occurring empty particle of a clinical C4 strain EV71
Components
  • Capsid protein VP0
  • Capsid protein VP1
  • Capsid protein VP3
KeywordsVIRUS / beta barrel / icosahedral virus / natually occurring empty particle with unknown function / replicate in host cell 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...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 / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / 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
Jelly Rolls - #20 / 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) ...Jelly Rolls - #20 / 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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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: 3.151 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 4, 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Q: Capsid protein VP1
I: Capsid protein VP1
M: Capsid protein VP1
A: Capsid protein VP1
R: Capsid protein VP3
J: Capsid protein VP3
N: Capsid protein VP3
B: Capsid protein VP3
S: Capsid protein VP0
K: Capsid protein VP0
O: Capsid protein VP0
C: Capsid protein VP0


Theoretical massNumber of molelcules
Total (without water)471,74615
Polymers471,74615
Non-polymers00
Water0
1
E: Capsid protein VP1
F: Capsid protein VP3
G: Capsid protein VP0
Q: Capsid protein VP1
I: Capsid protein VP1
M: Capsid protein VP1
A: Capsid protein VP1
R: Capsid protein VP3
J: Capsid protein VP3
N: Capsid protein VP3
B: Capsid protein VP3
S: Capsid protein VP0
K: Capsid protein VP0
O: Capsid protein VP0
C: 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 area1260920 Å2
ΔGint-6846 kcal/mol
Surface area1258020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)352.975, 352.975, 352.975
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), (0.3034, -0.8159, 0.4922, 0.808, 0.4941, 0.3209,-0.505, 0.3004, 0.8092, 1.689, -1.178, 0.6762), (-0.8062, 0.491, -0.3302, -0.5139, -0.3045, 0.802, 0.2932, 0.8162, 0.4978, 3.567, 0.5881, -0.3295), (-0.8135, -0.5065, 0.2856, 0.4827, -0.3143, 0.8174, -0.3243, 0.8029, 0.5002, 3.719, -0.6645, 0.4134) and (0.3089, 0.8069, -0.5034, -0.8107, 0.5002, 0.3043, 0.4974, 0.3141, 0.8087, 0.6959, 0.5791, -0.5132)

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Components

#1: Protein
Capsid protein VP1 /


Mass: 32699.773 Da / Num. of mol.: 5 / Mutation: K550Q / Source method: isolated from a natural source / Source: (natural) Enterovirus A71 / Strain: a clinical C4 strain / References: UniProt: F6KTB0
#2: Protein
Capsid protein VP3 /


Mass: 26440.148 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Enterovirus A71 / Strain: a clinical C4 strain / References: UniProt: F6KTB0
#3: Protein
Capsid protein VP0 /


Mass: 35209.219 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Enterovirus A71 / Strain: a clinical C4 strain / 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: 3.88 Å3/Da / Density % sol: 68.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Imidazole,1.0M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 2, 2010
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 3.151→49.918 Å / Num. all: 209079 / Num. obs: 190018 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.15→3.2 Å / Rmerge(I) obs: 0.904 / % possible all: 89.4

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.151→49.918 Å / σ(F): 1.34 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2336 2000 random
Rwork0.2165 --
all0.2169 128587 -
obs0.2169 109993 -
Refinement stepCycle: LAST / Resolution: 3.151→49.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26615 0 0 0 26615
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.897
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_dihedral_angle_d12.98
LS refinement shellResolution: 3.1511→3.2298 Å
RfactorNum. reflection% reflection
Rfree0.3188 147 -
Rwork0.3077 --
obs-7927 89 %

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