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- PDB-3zff: Human enterovirus 71 in complex with capsid binding inhibitor WIN51711 -

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Basic information

Entry
Database: PDB / ID: 3zff
TitleHuman enterovirus 71 in complex with capsid binding inhibitor WIN51711
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / INHIBITOR / CAPSID / PICORNAVIRUS
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 / nucleoside-triphosphate phosphatase ...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 / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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
Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / 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 ...Rhinovirus 14, subunit 4 - #370 / Rhinovirus 14, subunit 4 / 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 / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-W71 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHUMAN ENTEROVIRUS 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsPlevka, P. / Perera, R. / Yap, M.L. / Cardosa, J. / Kuhn, R.J. / Rossmann, M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure of Human Enterovirus 71 in Complex with a Capsid-Binding Inhibitor.
Authors: Plevka, P. / Perera, R. / Yap, M.L. / Cardosa, J. / Kuhn, R.J. / Rossmann, M.G.
History
DepositionDec 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _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

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9445
Polymers94,6014
Non-polymers3421
Water00
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,696,634300
Polymers5,676,088240
Non-polymers20,54660
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: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 475 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)474,71925
Polymers473,00720
Non-polymers1,7125
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 570 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)569,66330
Polymers567,60924
Non-polymers2,0556
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
Unit cell
Length a, b, c (Å)591.000, 591.000, 591.000
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(0.747381, 0.30937, 0.587947), (0.355598, 0.56121, -0.747365), (-0.561189, 0.767651, 0.309409)-270.85147, 345.88574, 278.7395
3generate(0.856193, -0.390229, -0.338542), (-0.148536, 0.441651, -0.884789), (0.494806, 0.807854, 0.320157)228.27844, 497.24753, 115.81137
4generate(0.561315, 0.747238, -0.3557), (-0.767593, 0.309411, -0.561267), (-0.309325, 0.588106, 0.747274)114.39999, 461.08868, 72.69092
5generate(0.441575, -0.807957, 0.390101), (0.884823, 0.320143, -0.338465), (0.148555, 0.494646, 0.856282)22.8231, 121.64268, -28.57565
6generate(0.309404, 0.561377, 0.767515), (-0.587981, 0.747288, -0.309529), (-0.74734, -0.355497, 0.561308)-324.24774, 259.55225, 355.0697
7generate(0.320132, -0.494603, 0.807988), (0.338493, 0.856297, 0.390043), (-0.884816, 0.148611, 0.441571)-191.55106, -202.35001, 355.67593
8generate(0.309404, -0.587981, -0.74734), (0.561377, 0.747288, -0.355497), (0.767515, -0.309529, 0.561308)518.30884, 114.29323, 129.92108
9generate(0.320132, 0.338493, -0.884816), (-0.494603, 0.856297, 0.148611), (0.807988, 0.390043, 0.441571)444.53491, 25.68392, 76.66245
10generate(0.441575, 0.884823, 0.148555), (-0.807957, 0.320143, 0.494646), (0.390101, -0.338465, 0.856282)-113.44968, -6.3661, 56.7576
11generate(0.561315, -0.767593, -0.309325), (0.747238, 0.309411, 0.588106), (-0.3557, -0.561267, 0.747274)312.19653, -270.90811, 245.17755
12generate(0.856193, -0.148536, 0.494806), (-0.390229, 0.441651, 0.807854), (-0.338542, -0.884789, 0.320157)-178.88412, -224.07645, 480.18558
13generate(0.747381, 0.355598, -0.561189), (0.30937, 0.56121, 0.767651), (0.587947, -0.747365, 0.309409)235.85646, -324.27945, 331.51779
14generate(0.884873, 0.31994, -0.338527), (-0.148678, -0.494705, -0.856226), (-0.441435, 0.808002, -0.390168)121.69286, 619.57721, 568.18011
15generate(0.69112, -0.21398, 0.69031), (0.542558, -0.47734, -0.691182), (0.47743, 0.852249, -0.21378)-232.97305, 443.62775, 350.45007
16generate(0.000161, 1, -0.000147), (1.4E-5, -0.000147, -1), (-1, 0.000161, -1.4E-5)0.0423, 591.0191, 590.98322
17generate(-0.176232, -0.017348, 0.984196), (0.965121, 0.193609, 0.176229), (-0.193606, 0.980925, -0.017377)-267.51556, -101.62711, 340.94232
18generate(-0.017521, -0.984196, 0.176215), (0.193738, -0.176243, -0.965092), (0.980897, 0.01723, 0.193764)210.02367, 572.88147, 216.2059
19generate(0.193592, -0.176405, -0.965093), (-0.980925, -0.017219, -0.19362), (0.017538, 0.984167, -0.176373)572.9259, 374.73215, 381.04874
20generate(-0.390041, 0.441757, 0.807887), (0.338612, 0.884722, -0.320268), (-0.856251, 0.14862, -0.494681)-224.13339, 110.86382, 769.82428
21generate(-0.21397, -0.690268, -0.691164), (-0.477151, 0.69126, -0.542625), (0.852357, 0.213662, -0.477289)583.46405, 355.78271, 506.20572
22generate(-0.49467, 0.856294, 0.148403), (-0.80791, -0.390163, -0.441605), (-0.320224, -0.338361, 0.884834)25.78661, 514.35925, 146.45132
23generate(-0.47731, -0.85229, 0.213881), (0.691117, -0.213773, 0.690376), (-0.542667, 0.477359, 0.691084)240.49347, -233.0325, 147.42896
24generate(-0.49467, -0.807911, -0.320224), (0.856294, -0.390163, -0.338361), (0.148403, -0.441605, 0.884834)475.20724, 228.17332, 93.7449
25generate(-0.47731, 0.691117, -0.542667), (-0.85229, -0.213773, 0.477359), (0.213881, 0.690376, 0.691084)355.84473, 84.76958, 7.56918
26generate(-0.21397, -0.477151, 0.852357), (-0.690268, 0.69126, 0.213662), (-0.691164, -0.542625, -0.477289)-136.84637, 48.65353, 837.95312
27generate(-0.390041, 0.338612, -0.856251), (0.441757, 0.884722, 0.14862), (0.807887, -0.320268, -0.494681)534.19873, -113.49045, 597.40955
28generate(-0.017521, 0.193738, 0.980897), (-0.984196, -0.176243, 0.01723), (0.176215, -0.965092, 0.193764)-319.38501, 303.94577, 473.98132
29generate(0.193592, -0.980925, 0.017538), (-0.176405, -0.017219, 0.984167), (-0.965092, -0.19362, -0.176373)249.98778, -267.49655, 692.68903
30generate(0.000161, 1.4E-5, -1), (1, -0.000147, 0.000161), (-0.000147, -1, -1.4E-5)590.97467, -0.05081, 591.02759
31generate(-0.176232, 0.965121, -0.193606), (-0.017348, 0.193609, 0.980925), (0.984196, 0.176229, -0.017377)116.94626, -319.40402, 287.12186
32generate(0.69112, 0.542558, 0.47743), (-0.213981, -0.47734, 0.852249), (0.690309, -0.691182, -0.21378)-246.99979, -136.76932, 542.38208
33generate(0.884873, -0.148678, -0.441435), (0.31994, -0.494705, 0.808002), (-0.338527, -0.856227, -0.390168)235.26495, -191.51489, 793.40063
34generate(0.338674, 0.856195, 0.390108), (0.884771, -0.148743, -0.441616), (-0.320065, 0.494739, -0.807931)-202.39078, 235.37007, 782.49658
35generate(0.623557, -0.779963, -0.052948), (-0.63059, -0.461765, -0.623771), (0.462054, 0.422357, -0.779792)190.46603, 580.49194, 667.54578
36generate(-0.148471, 0.441469, -0.88489), (-0.494772, -0.807924, -0.320032), (-0.856224, 0.390288, 0.338395)497.3096, 475.13803, 362.7832
37generate(-0.461963, -0.42249, 0.779774), (0.623724, -0.779827, -0.052982), (0.630492, 0.461873, 0.62379)-76.53203, 190.43761, 10.49808
38generate(-0.807943, 0.320335, 0.494545), (-0.389976, 0.33843, -0.856352), (-0.441711, -0.884767, -0.148487)-6.35042, 534.26074, 704.43103
39generate(-0.779855, -0.461775, 0.422546), (0.053071, 0.62383, 0.779737), (-0.623682, 0.630525, -0.461975)134.58257, -301.74033, 652.15009
40generate(-0.807943, -0.389976, -0.441711), (0.320335, 0.33843, -0.884767), (0.494545, -0.856352, -0.148487)514.38428, 444.49268, 565.27734
41generate(-0.779855, 0.053071, -0.623682), (-0.461775, 0.62383, 0.630525), (0.422546, 0.779737, -0.461975)527.71838, -160.81345, 479.70792
42generate(-0.461963, 0.623724, 0.630492), (-0.42249, -0.779827, 0.461873), (0.779774, -0.052982, 0.62379)-160.7565, 111.34238, 63.23193
43generate(-0.148471, -0.494772, -0.856224), (0.441469, -0.807924, 0.390288), (-0.88489, -0.320032, 0.338395)619.55573, 22.74985, 469.38199
44generate(0.623557, -0.63059, 0.462054), (-0.779963, -0.461765, 0.422357), (-0.052948, -0.623771, -0.779792)-61.15807, 134.68109, 892.73877
45generate(0.338674, 0.884771, -0.320065), (0.856195, -0.148743, 0.494739), (0.390108, -0.441616, -0.807931)110.75706, -178.82468, 815.12341
46generate(0.965121, 0.193462, 0.17639), (0.193462, -0.980954, 0.017365), (0.17639, 0.017365, -0.984167)-101.67792, 250.08781, 858.47748
47generate(0.355801, 0.561148, -0.747316), (0.561148, -0.767729, -0.30929), (-0.747316, -0.30929, -0.588072)345.84351, 312.22495, 861.88635
48generate(0.053037, 0.623663, 0.779872), (0.623663, -0.630623, 0.461866), (0.779872, 0.461866, -0.422414)-301.77203, -61.08481, 456.34262
49generate(0.218379, -0.285478, 0.933153), (-0.285478, -0.933094, -0.218631), (0.933153, -0.218631, -0.285285)-262.95724, 417.70242, 471.13132
50generate(0.5426, -0.477499, -0.691039), (-0.477499, -0.852182, 0.213891), (-0.691039, 0.213891, -0.690418)443.58109, 240.50058, 824.02271
51generate(-0.587822, 0.74743, -0.309488), (0.74743, 0.355395, -0.561252), (-0.309488, -0.561252, -0.767573)259.49023, 235.90663, 915.2677
52generate(-0.690201, 0.691262, 0.213869), (0.691262, 0.542517, 0.47727), (0.213869, 0.47727, -0.852316)48.55083, -246.94315, 727.82532
53generate(-0.422679, -0.779719, 0.461883), (-0.779719, 0.053105, -0.623849), (0.461883, -0.623849, -0.630427)111.34949, 527.76849, 751.75671
54generate(-0.28558, -0.933108, -0.218439), (-0.933108, 0.218764, 0.285331), (-0.218439, 0.285331, -0.933184)417.63321, 119.82271, 854.00098
55generate(-0.767457, 0.309445, -0.561434), (0.309445, -0.588141, -0.747197), (-0.561434, -0.747197, 0.355598)461.13876, 518.26215, 476.65646
56generate(-0.933122, 0.218572, 0.285432), (0.218572, -0.285376, 0.933139), (0.285432, 0.933139, 0.218498)119.80702, -262.99341, 173.35696
57generate(-0.852399, -0.213763, 0.47717), (-0.213763, -0.690335, -0.691162), (0.47717, -0.691162, 0.542734)84.8681, 583.44257, 235.15201
58generate(-0.630558, -0.461953, -0.623665), (-0.461953, -0.422301, 0.779883), (-0.623665, 0.779883, 0.052859)580.46704, -76.60909, 400.60107
59generate(-0.980897, -0.017391, -0.19375), (-0.017391, -0.984167, 0.176388), (-0.19375, 0.176388, 0.965064)374.81085, 209.92363, 18.11218
60generate(-0.984224, -0.176071, 0.01736), (-0.176071, 0.965121, -0.193753), (0.01736, -0.193753, -0.980897)303.86707, 116.98856, 910.41034

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Components

#1: Protein VP1


Mass: 32775.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ENTEROVIRUS 71 / Variant: ISOLATE MY104-9-SAR-97 / References: UniProt: A9X4C2
#2: Protein VP2


Mass: 27800.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ENTEROVIRUS 71 / Variant: ISOLATE MY104-9-SAR-97 / References: UniProt: A9X4C2
#3: Protein VP3


Mass: 26524.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ENTEROVIRUS 71 / Variant: ISOLATE MY104-9-SAR-97 / References: UniProt: A9X4C2
#4: Protein VP4


Mass: 7501.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HUMAN ENTEROVIRUS 71 / Variant: ISOLATE MY104-9-SAR-97 / References: UniProt: A9X4C2, UniProt: B2ZUN0*PLUS
#5: Chemical ChemComp-W71 / 5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE / COMPOUND IV


Mass: 342.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N2O3
Nonpolymer details5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE (W71): WIN51711

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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: 4.55 Å3/Da / Density % sol: 73 % / Description: NONE
Crystal growpH: 8.5
Details: THE CRYSTALLIZATION DROPS WERE PREPARED BY MIXING 0.83UL OF EV71 AT 2MG/ML IN PBS WITH 0.17UL OF 0.2M SODIUM CITRATE, 0.1M TRIS PH8.5, 30% V/V PEG 400. THE WELL SOLUTION CONTAINED 1.8M ...Details: THE CRYSTALLIZATION DROPS WERE PREPARED BY MIXING 0.83UL OF EV71 AT 2MG/ML IN PBS WITH 0.17UL OF 0.2M SODIUM CITRATE, 0.1M TRIS PH8.5, 30% V/V PEG 400. THE WELL SOLUTION CONTAINED 1.8M SODIUM ACETATE AND 0.1M BIS-TRIS PROPANE PH7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.4→27.5 Å / Num. obs: 247559 / % possible obs: 53.3 % / Observed criterion σ(I): 0.9 / Redundancy: 1.8 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 2.6
Reflection shellResolution: 3.4→3.55 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.06 / % possible all: 27.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
GLRFphasing
PHASERphasing
CNS1.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AED

4aed


Resolution: 3.4→27.5 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0
Isotropic thermal model: CONSTRAINED 2 B FACTORS PER RESIDUE
Cross valid method: NONE / σ(F): 0.9
RfactorNum. reflection% reflection
Rwork0.2434 --
obs0.2434 247559 53.3 %
Solvent computationSolvent model: BULK SOLVENT
Displacement parametersBiso mean: 30.6 Å2
Refinement stepCycle: LAST / Resolution: 3.4→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6507 0 25 0 6532
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008399
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.49045
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTRAINS
LS refinement shellResolution: 3.4→3.55 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.3443 12721 -
obs--27.5 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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