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- PDB-3vdd: Structure of HRV2 capsid complexed with antiviral compound BTA798 -

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Basic information

Entry
Database: PDB / ID: 3vdd
TitleStructure of HRV2 capsid complexed with antiviral compound BTA798
Components
  • Protein VP1
  • Protein VP2
  • Protein VP3
  • Protein VP4
KeywordsVIRUS / viral capsid / virus-drug complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / 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 / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / 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 / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / 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 / proteolysis / RNA binding / ATP binding / membrane / 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. / 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-BT8 / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsMorton, C.J. / Feil, S.C. / Parker, M.W.
CitationJournal: ACS Med Chem Lett / Year: 2012
Title: An Orally Available 3-Ethoxybenzisoxazole Capsid Binder with Clinical Activity against Human Rhinovirus.
Authors: Feil, S.C. / Hamilton, S. / Krippner, G.Y. / Lin, B. / Luttick, A. / McConnell, D.B. / Nearn, R. / Parker, M.W. / Ryan, J. / Stanislawski, P.C. / Tucker, S.P. / Watson, K.G. / Morton, C.J.
History
DepositionJan 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Sep 13, 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_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_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: Protein VP1
B: Protein VP2
C: Protein VP3
D: Protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2625
Polymers94,8804
Non-polymers3821
Water21612
1
A: Protein VP1
B: Protein VP2
C: Protein VP3
D: Protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,715,726300
Polymers5,692,779240
Non-polymers22,94760
Water3,243180
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: Protein VP1
B: Protein VP2
C: Protein VP3
D: Protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 476 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)476,31125
Polymers474,39820
Non-polymers1,9125
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Protein VP1
B: Protein VP2
C: Protein VP3
D: Protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 572 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)571,57330
Polymers569,27824
Non-polymers2,2956
Water32418
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: Protein VP1
B: Protein VP2
C: Protein VP3
D: Protein VP4
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.86 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)2,857,863150
Polymers2,846,389120
Non-polymers11,47430
Water1,62190
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)310.490, 345.680, 378.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.31029999, -0.81770003, -0.4849), (0.80110002, 0.49959999, -0.32980001), (0.51190001, -0.2861, 0.81)-162.821, -106.4606, -61.2899
3generate(-0.80699998, -0.52609998, -0.26840001), (0.47530001, -0.30860001, -0.82389998), (0.3506, -0.7924, 0.4991)-96.6498, -269.72601, -163.7545
4generate(-0.80930001, 0.472, 0.3495), (-0.5219, -0.30509999, -0.79659998), (-0.2694, -0.82709998, 0.49329999)107.0634, -263.54031, -167.4771
5generate(0.30919999, 0.79790002, 0.51749998), (-0.81629997, 0.50190002, -0.28600001), (-0.48800001, -0.3339, 0.80650002)167.0174, -97.003, -65.4118
6generate(0.79070002, 0.52530003, -0.31439999), (0.52249998, -0.31150001, 0.79369998), (0.31900001, -0.79189998, -0.52079999)140.8598, -135.74339, -167.23599
7generate(0.49990001, -0.292, -0.8154), (0.3265, -0.80849999, 0.48969999), (-0.80220002, -0.51099998, -0.30880001)-24.5268, -236.0479, -103.0643
8generate(-0.498, -0.32089999, -0.80559999), (-0.29409999, -0.81150001, 0.505), (-0.81580001, 0.48840001, 0.3098)-24.6766, -233.21339, 100.9522
9generate(-0.82690001, 0.4747, -0.30149999), (-0.47670001, -0.3073, 0.82359999), (0.2983, 0.82480001, 0.4804)139.73891, -129.1174, 162.8176
10generate(-0.0351, 0.99940002, 0.0028), (0.0327, -0.0016, 0.99949998), (0.99879998, 0.0352, -0.0326)242.28371, -69.6166, -2.6227
11generate(0.50260001, 0.2922, -0.8136), (-0.32409999, -0.80879998, -0.49070001), (-0.80140001, 0.51029998, -0.3118)26.1198, -421.78781, -14.2248
12generate(-0.0331, -0.0309, -0.99900001), (-0.99940002, -0.0017, 0.0332), (-0.0027, 0.99949998, -0.0308)-36.8238, -252.8275, 81.0745
13generate(-0.54839998, 0.29440001, -0.7827), (-0.29409999, 0.80830002, 0.51010001), (0.78280002, 0.50989997, -0.35659999)32.6479, -91.9254, -23.351
14generate(-0.3414, 0.81940001, -0.46059999), (0.81690001, 0.50099999, 0.28580001), (0.46489999, -0.27869999, -0.84039998)138.7305, -161.1512, -182.8203
15generate(0.3116, 0.81980002, -0.4804), (0.79970002, -0.4993, -0.33340001), (-0.51319999, -0.28029999, -0.81120002)134.98511, -365.2569, -177.3757
16generate(0.3141, -0.79909998, 0.5126), (-0.81620002, -0.50309998, -0.28400001), (0.48480001, -0.3292, -0.81029999)-127.0661, -356.3114, -181.4416
17generate(-0.27700001, -0.80140001, 0.53009999), (-0.8003, 0.49770001, 0.3344), (-0.53179997, -0.33160001, -0.77920002)-124.0179, -152.2401, -175.8726
18generate(-0.45159999, -0.32609999, 0.83050001), (0.32319999, 0.80779999, 0.49290001), (-0.83160001, 0.491, -0.25940001)-25.9311, -95.5085, -6.0945
19generate(0.0305, -0.0317, 0.99900001), (0.99949998, 0.001, -0.0304), (-0.0001, 0.99949998, 0.0317)31.3724, -264.3783, 92.8825
20generate(0.4984, -0.32319999, 0.80449998), (0.29440001, -0.80970001, -0.50760001), (0.8154, 0.48980001, -0.30840001)-30.9122, -425.4306, -15.9131
21generate(-0.99809998, -0.0019, 0.0615), (0.0019, -1, -0.0012), (0.0615, -0.001, 0.99809998)11.509, -519.7276, -0.5086
22generate(-0.27869999, 0.7974, 0.53530002), (-0.79970002, -0.50129998, 0.3303), (0.53179997, -0.336, 0.77740002)170.3912, -413.36569, -71.5468
23generate(0.82810003, 0.47440001, 0.29859999), (-0.47400001, 0.30829999, 0.82480001), (0.2992, -0.82459998, 0.48019999)97.7299, -249.77271, -169.987
24generate(0.7906, -0.52340001, -0.3177), (0.5226, 0.3064, 0.7956), (-0.31909999, -0.79509997, 0.5158)-105.6284, -255.901, -160.43761
25generate(-0.33840001, -0.81779999, -0.46560001), (0.81669998, -0.50099999, 0.28639999), (-0.46740001, -0.28330001, 0.83740002)-158.9673, -422.4238, -55.14
26generate(-0.54799998, -0.2906, -0.78439999), (0.29409999, 0.81089997, -0.50590003), (0.78310001, -0.5079, -0.35890001)-18.1745, -284.29721, -112.0307
27generate(-0.80699998, 0.52530003, -0.26989999), (0.47620001, 0.30860001, -0.82340002), (-0.3493, -0.79299998, -0.49919999)149.9518, -387.98779, -163.448
28generate(0.0285, 0.99959999, 0.0012), (-0.0312, 0.0021, -0.99949998), (-0.99910003, 0.0284, 0.0312)241.8501, -447.61469, 8.1447
29generate(0.80860001, 0.47530001, -0.3468), (-0.52319998, 0.31099999, -0.79339999), (-0.2692, 0.82300001, 0.50019997)130.29491, -381.65289, 166.0231
30generate(0.44960001, -0.32269999, -0.83289999), (-0.3256, 0.80909997, -0.4892), (0.83179998, 0.4912, 0.25870001)-30.5925, -281.11859, 91.6155

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Protein VP1 / capsid VP1 / P1D / Virion protein 1


Mass: 32274.100 Da / Num. of mol.: 1 / Fragment: UNP residues 568-850 / Source method: isolated from a natural source / Details: Tissue culture / Source: (natural) Human rhinovirus 2 / References: UniProt: P04936
#2: Protein Protein VP2 / capsid VP2 / P1B / Virion protein 2


Mass: 29009.588 Da / Num. of mol.: 1 / Fragment: UNP residues 70-330 / Source method: isolated from a natural source / Details: Tissue culture / Source: (natural) Human rhinovirus 2 / References: UniProt: P04936
#3: Protein Protein VP3 / capsid VP3 / P1C / Virion protein 3


Mass: 26107.793 Da / Num. of mol.: 1 / Fragment: UNP residues 331-567 / Source method: isolated from a natural source / Details: Tissue culture / Source: (natural) Human rhinovirus 2 / References: UniProt: P04936
#4: Protein Protein VP4 / capsid VP4 / P1A / Virion protein 4


Mass: 7488.167 Da / Num. of mol.: 1 / Fragment: UNP residues 1-69 / Source method: isolated from a natural source / Details: Tissue culture / Source: (natural) Human rhinovirus 2 / References: UniProt: P04936

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Non-polymers , 2 types, 13 molecules

#5: Chemical ChemComp-BT8 / 3-ethoxy-6-{2-[1-(6-methylpyridazin-3-yl)piperidin-4-yl]ethoxy}-1,2-benzoxazole / BTA798


Mass: 382.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N4O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.52 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 0.4-0.7 M ammonium sulfate, pH 7.5, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9999 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 13, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.2→25 Å / Num. obs: 660217 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 55.35 Å2 / Rmerge(I) obs: 0.252 / Net I/σ(I): 10.6
Reflection shellResolution: 3.2→3.28 Å / Redundancy: 10 % / Mean I/σ(I) obs: 1.97 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å24.94 Å
Translation4 Å24.94 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.3.0phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FPN

1fpn


Resolution: 3.2→24.942 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.47 / σ(F): 1.99 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2727 33012 5 %
Rwork0.2295 --
obs0.2317 660217 99.89 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.63 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 407.3 Å2 / Biso mean: 50.6585 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--0.5375 Å20 Å2-0 Å2
2--11.8152 Å2-0 Å2
3----17.1167 Å2
Refinement stepCycle: LAST / Resolution: 3.2→24.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6340 0 28 12 6380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021196200
X-RAY DIFFRACTIONf_angle_d1.97267810
X-RAY DIFFRACTIONf_chiral_restr0.13429880
X-RAY DIFFRACTIONf_plane_restr0.00934410
X-RAY DIFFRACTIONf_dihedral_angle_d19.59170740
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.23630.39310960.3442083221928100
3.2363-3.27430.378610940.33832077421868100
3.2743-3.31410.372810920.31952076321855100
3.3141-3.3560.365110950.31082079821893100
3.356-3.40.375510960.30912083121927100
3.4-3.44650.350810960.29762082021916100
3.4465-3.49560.34710970.29772084321940100
3.4956-3.54760.336110940.28352077621870100
3.5476-3.60290.33710980.28412087021968100
3.6029-3.66180.333110940.27592078421878100
3.6618-3.72470.311210950.27252079921894100
3.7247-3.79220.311111000.26372090222002100
3.7922-3.86490.319710960.25842082221918100
3.8649-3.94350.311110990.25892088821987100
3.9435-4.02890.2910970.23962083921936100
4.0289-4.12220.283410970.2382085021947100
4.1222-4.22480.267710990.22672086521964100
4.2248-4.33850.259911000.21242091622016100
4.3385-4.46550.253110990.20612088121980100
4.4655-4.60870.230811020.19712093422036100
4.6087-4.77230.234611000.19172088721987100
4.7723-4.9620.231411030.18822096522068100
4.962-5.18590.230311030.18742095922062100
5.1859-5.45660.226711050.18592098722092100
5.4566-5.79450.229111040.1932098422088100
5.7945-6.23540.225711080.18992105622164100
6.2354-6.85110.216511100.18382108422194100
6.8511-7.81560.20711140.17192116622280100
7.8156-9.74810.176511200.15142128022400100
9.7481-24.94280.227511090.2082210502215997

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