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- PDB-4n43: Human enterovirus 71 uncoating intermediate captured at atomic re... -

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Basic information

Entry
Database: PDB / ID: 4n43
TitleHuman enterovirus 71 uncoating intermediate captured at atomic resolution
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
KeywordsVIRUS / hand-foot-and-mouth disease / picornavirus / human enterovirus 71 / uncoating intermediate / icosahedral virus / pocket factor
Function / homology
Function and homology information


RNA-protein covalent cross-linking / : / 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 ...RNA-protein covalent cross-linking / : / 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 / RNA binding / ATP binding / metal ion binding / nucleus
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) / 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
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8011 Å
AuthorsChen, R. / Lyu, K.
CitationJournal: J.Virol. / Year: 2014
Title: Human enterovirus 71 uncoating captured at atomic resolution.
Authors: Lyu, K. / Ding, J. / Han, J.F. / Zhang, Y. / Wu, X.Y. / He, Y.L. / Qin, C.F. / Chen, R.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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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 VP2
C: Capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)86,8663
Polymers86,8663
Non-polymers00
Water0
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,211,963180
Polymers5,211,963180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
x 5


  • icosahedral pentamer
  • 434 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)434,33015
Polymers434,33015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
x 6


  • icosahedral 23 hexamer
  • 521 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)521,19618
Polymers521,19618
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
x 5


  • crystal asymmetric unit, crystal frame
  • 434 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)434,33015
Polymers434,33015
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)352.416, 352.416, 352.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number208
Space group name H-MP4232
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.8061, -0.3007, 0.5098), (0.3233, 0.4978, 0.8048), (-0.4957, 0.8135, -0.304)-2.178, 0.8541, -0.9792
3generate(-0.8081, 0.3247, -0.4914), (-0.2954, 0.4984, 0.8151), (0.5096, 0.8038, -0.3069)-3.055, -0.2166, 0.6471
4generate(0.3163, 0.5098, -0.8), (-0.4924, 0.809, 0.3209), (0.8109, 0.2924, 0.5069)-2.156, -1.067, 1.789
5generate(0.313, -0.5003, 0.8073), (0.5116, 0.805, 0.3005), (-0.8002, 0.3189, 0.5079)0.08526, 1.261, -2.086

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Components

#1: Protein Capsid protein VP1 /


Mass: 32699.773 Da / Num. of mol.: 1 / Fragment: EV71 capsid protein VP1 / Source method: isolated from a natural source
Details: isolated in Fuyang, Anhui in 2008, grow in RD cells
Source: (natural) Enterovirus A71
Strain: clinical C4 strain, AH08/06, GenBank accession no. HQ611148
References: UniProt: M9XM90
#2: Protein Capsid protein VP2 /


Mass: 27726.135 Da / Num. of mol.: 1 / Fragment: EV71 capsid protein VP2 / Source method: isolated from a natural source
Details: isolated in Fuyang, Anhui in 2008, grow in RD cells
Source: (natural) Enterovirus A71
Strain: clinical C4 strain, AH08/06, GenBank accession no. HQ611148
References: UniProt: Q9WQJ0
#3: Protein Capsid protein VP3 /


Mass: 26440.148 Da / Num. of mol.: 1 / Fragment: EV71 capsid protein VP3 / Source method: isolated from a natural source
Details: isolated in Fuyang, Anhui in 2008, grow in RD cells
Source: (natural) Enterovirus A71
Strain: clinical C4 strain, AH08/06, GenBank accession no. HQ611148
References: UniProt: Q9WPJ0

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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: 4.2 Å3/Da / Density % sol: 70.71 %
Crystal growTemperature: 289 K / pH: 7
Details: 0.1M Cacodylate containing 1.6M Sodium Acetate, pH 7.0, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 3.801→49.84 Å / Num. all: 73630 / Num. obs: 50069 / % possible obs: 68 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.384 / Χ2: 1.307 / Net I/σ(I): 2.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3.801-3.874.60.8391.3426520.82573.4
3.87-3.944.70.7811.4426530.81773.4
3.94-4.014.70.7541.526370.8372.9
4.01-4.094.80.631.8126290.86172.1
4.09-4.184.80.562.0626110.88872.4
4.18-4.284.80.522.1625870.88971.2
4.28-4.394.90.4432.6225530.9270.6
4.39-4.54.90.4372.825581.01370.4
4.5-4.644.90.4113.0425441.04569.5
4.64-4.794.90.3823.4225201.0969.1
4.79-4.9650.3833.3324951.06668.3
4.96-5.1650.3593.7625081.17568.6
5.16-5.3950.3783.3624881.07367.9
5.39-5.6750.3873.5524771.15267.3
5.67-6.035.10.4063.3924411.09866.4
6.03-6.4950.3723.7924461.0965.9
6.49-7.155.10.324.7224001.25164.6
7.15-8.185.20.2586.6423381.46462
8.18-10.295.50.18713.0422992.46360.6
10.29-505.60.1719.4822654.90856.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1POV

1pov


Resolution: 3.8011→49.84 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2741 1998 -RANDOM
Rwork0.2454 ---
all0.2466 73598 --
obs0.2466 50069 68.03 %-
Displacement parametersBiso max: 182.55 Å2 / Biso mean: 47.4384 Å2 / Biso min: 13.29 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 3.8011→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5259 0 0 0 5259
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.641
X-RAY DIFFRACTIONf_dihedral_angle_d12.198
X-RAY DIFFRACTIONf_chiral_restr0.027
X-RAY DIFFRACTIONf_plane_restr0.003
LS refinement shellResolution: 3.8011→3.8961 Å
RfactorNum. reflection
Rfree0.3293 150
Rwork0.2973 -
obs-3779

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