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- PDB-4rr3: Crystal structure of a recombinant EV71 virus particle -

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Basic information

Entry
Database: PDB / ID: 4rr3
TitleCrystal structure of a recombinant EV71 virus particle
Components
  • Capsid protein VP0
  • Capsid protein VP1
  • Capsid protein VP3
KeywordsVIRUS / beta barrel / eight-stranded beta barrel / replicate in the 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: 3.103 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 6, 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 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)475,74615
Polymers475,74615
Non-polymers00
Water00
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)5,708,949180
Polymers5,708,949180
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 area1309140 Å2
ΔGint-7319 kcal/mol
Surface area1263490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)350.599, 350.599, 350.599
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), (0.3038, -0.8069, 0.5066, 0.804, 0.5025, 0.3181, -0.5112, 0.3106, 0.8014, -0.9474, -1.348, 0.9465), (-0.8079, 0.4819, -0.3392, -0.5134, -0.2927, 0.8067, 0.2895, 0.8259, 0.4839, 5.429, -0.9913, 0.9334), (-0.8132, -0.5063, 0.287, 0.4827, -0.3113, 0.8186, -0.3251, 0.8042, 0.4975, 3.379, -1.134, 0.6254) and (0.3056, 0.8031, -0.5116, -0.8063, 0.504, 0.3097, 0.5065, 0.3179, 0.8015, 2.154, -0.4491, 0.1634).

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Components

#1: Protein
Capsid protein VP1


Mass: 33499.781 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 VP3


Mass: 26440.148 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 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

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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: 3.77 Å3/Da / Density % sol: 67.41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Imidazole containing 1M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97803 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2012
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97803 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 131863 / % possible obs: 90.72 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6498 / % possible all: 100

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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: 3.103→46.438 Å / σ(F): 1.33 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2652 1995 random
Rwork0.2354 --
all0.2358 131863 -
obs0.2358 131665 -
Refinement stepCycle: LAST / Resolution: 3.103→46.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27390 0 0 0 27390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.006
X-RAY DIFFRACTIONf_bond_d1.131
X-RAY DIFFRACTIONf_dihedral_angle_d14.168
LS refinement shellResolution: 3.1034→3.181 Å
RfactorNum. reflection% reflection
Rfree0.3343 141 -
Rwork0.3353 --
obs-9151 100 %

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