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- PDB-4n53: Human enterovirus 71 uncoating intermediate captured at atomic re... -

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Basic information

Entry
Database: PDB / ID: 4n53
TitleHuman enterovirus 71 uncoating intermediate captured at atomic resolution
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
  • Capsid protein VP4
KeywordsVIRUS / hand-foot-and-mouth disease / human enterovirus 71 / virion / pocket factor / picornavirus / icosahedral virus
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 / endocytosis involved in viral entry into host cell ...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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / host cell cytoplasm / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont entry into host cell / 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 / structural molecule activity / virion attachment to host cell / RNA binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / 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 ...Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / 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 / Few Secondary Structures / Irregular / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
SPHINGOSINE / Genome polyprotein / Genome polyprotein / Genome polyprotein / Capsid protein VP0
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3063 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 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Sep 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
D: Capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6675
Polymers94,3674
Non-polymers2991
Water0
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,680,003300
Polymers5,662,033240
Non-polymers17,97060
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
D: Capsid protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 473 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)473,33425
Polymers471,83620
Non-polymers1,4975
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 568 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)568,00030
Polymers566,20324
Non-polymers1,7976
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
D: Capsid protein VP4
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.89 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,893,334100
Polymers1,887,34480
Non-polymers5,99020
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)591.375, 591.375, 591.375
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.7415, -0.5939, 0.312), (0.5685, 0.3093, -0.7623), (0.3563, 0.7427, 0.567)78.08, 128.2, -96.09
3generate(0.3274, -0.39, 0.8607), (0.3236, -0.8095, -0.4899), (0.8877, 0.4389, -0.1388)29.43, 285.7, -27.25
4generate(0.3287, 0.319, 0.8889), (-0.3951, -0.8085, 0.4362), (0.8578, -0.4946, -0.1397)-77.19, 254.8, 111.8
5generate(0.7418, 0.5655, 0.3604), (-0.5959, 0.3093, 0.7411), (0.3077, -0.7645, 0.5664)-96.18, 78.24, 128.4
6generate(0.03339, -0.7772, 0.6284), (-0.7736, -0.4182, -0.4762), (0.6329, -0.4702, -0.6152)160.6, 384.6, 210.2
7generate(-0.1883, 0.2065, 0.9602), (-0.9819, -0.01866, -0.1886), (-0.02102, -0.9783, 0.2062)2.892, 315.7, 258.7
8generate(0.3207, 0.8885, 0.3281), (-0.8064, 0.4379, -0.3976), (-0.4969, -0.1371, 0.8569)-77.62, 254.7, 111.7
9generate(0.859, 0.3272, -0.3937), (-0.4924, 0.3176, -0.8104), (-0.1401, 0.89, 0.4339)30.03, 286.2, -27.1
10generate(0.6812, -0.7013, -0.2101), (-0.4746, -0.2045, -0.8561), (0.5574, 0.6829, -0.4721)177.2, 365.4, 33.79
11generate(0.3123, 0.7459, -0.5883), (-0.7652, 0.5645, 0.3095), (0.563, 0.3536, 0.747)77.25, 128.5, -95.29
12generate(0.4426, -0.3932, -0.8059), (-0.1352, 0.8592, -0.4935), (0.8865, 0.3274, 0.3271)254.1, 111.4, -77.56
13generate(-0.1858, -0.9824, -0.01935), (0.2084, -0.02016, -0.9778), (0.9602, -0.1857, 0.2084)315.8, 258.6, 2.711
14generate(-0.7039, -0.2073, 0.6794), (-0.2067, -0.8553, -0.4751), (0.6796, -0.4748, 0.5592)177.2, 366.2, 34.19
15generate(-0.3964, 0.8584, 0.3256), (-0.8066, -0.495, 0.323), (0.4384, -0.1346, 0.8886)30.24, 285.8, -27.37
16generate(-0.8544, -0.4754, -0.2097), (0.4765, -0.556, -0.6811), (0.2072, -0.6819, 0.7015)70.69, 261.5, 118.6
17generate(-0.9781, 0.2072, -0.01804), (-0.2069, -0.9605, 0.186), (0.02121, 0.1857, 0.9824)-37.29, 292.9, -20.08
18generate(-0.6164, 0.6304, -0.4719), (-0.6315, -0.03788, 0.7744), (0.4703, 0.7754, 0.4215)-85.22, 135.8, -89.06
19generate(-0.2739, 0.2091, -0.9388), (-0.2113, 0.9392, 0.2708), (0.9383, 0.2725, -0.2131)-6.836, 7.089, 7.126
20generate(-0.4181, -0.468, -0.7786), (0.4738, 0.619, -0.6264), (0.7751, -0.6308, -0.0371)88.59, 84.61, 135.8
DetailsThe asymmetric unit contains 20 copies of the protomer. Each protomer consists of one copy each of VP1, VP2, VP3 and VP4. The biological assembly contains 60 copies of the protomer.

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Components

#1: Protein Capsid protein VP1 /


Mass: 32699.773 Da / Num. of mol.: 1 / 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: S5QA87
#2: Protein Capsid protein VP2 /


Mass: 27726.135 Da / Num. of mol.: 1 / 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: S4VM80
#3: Protein Capsid protein VP3 /


Mass: 26440.148 Da / Num. of mol.: 1 / 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: S5ZCI0
#4: Protein Capsid protein VP4 /


Mass: 7501.162 Da / Num. of mol.: 1 / 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: S6C3M9
#5: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2

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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

Crystal growTemperature: 289 K / Method: hanging drop / pH: 4.5
Details: 0.1M Sodium Acetate containing 3.5M Sodium Formate, pH 4.5, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.306→48.286 Å / Num. all: 505463 / Num. obs: 314499 / % possible obs: 62.22 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 1.5 % / Rmerge(I) obs: 0.216 / Χ2: 2.289 / Net I/σ(I): 4.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
3.306-3.381.20.7010.93154901.32946.2
3.38-3.461.20.5751.17152941.35745.5
3.46-3.551.20.5081.4150901.48744.9
3.55-3.661.20.4071.77152421.53245.5
3.66-3.781.20.3392.23156651.67146.6
3.78-3.911.20.342.41166981.76449.7
3.91-4.071.30.2942.79180121.97753.5
4.07-4.251.30.2743.32196502.32558.5
4.25-4.481.40.2464.25213172.64863.3
4.48-4.761.50.2414.6231332.8568.8
4.76-5.131.60.2394.76255382.72775.6
5.13-5.641.70.2324.63275642.22781.7
5.64-6.461.80.2084.97289601.90385.8
6.46-8.131.90.1846.17291922.10586.2
8.13-5020.1439.74277582.84680.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D4M

1d4m


Resolution: 3.3063→48.286 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 2011 -RANDOM
Rwork0.228 ---
all0.2282 505463 --
obs0.2282 314499 62.22 %-
Displacement parametersBiso max: 116.42 Å2 / Biso mean: 50.47 Å2 / Biso min: 0 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 3.3063→48.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6515 0 21 0 6536
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfond length0.003
X-RAY DIFFRACTIONfond angle0.728
X-RAY DIFFRACTIONfhirality0.029
X-RAY DIFFRACTIONflanarity0.004
X-RAY DIFFRACTIONfihedral13.125
LS refinement shellResolution: 3.3063→3.389 Å
RfactorNum. reflection
Rfree0.3504 107
Rwork0.323 -
obs-16521

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