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- PDB-4pdw: A benzonitrile analogue inhibits rhinovirus replication -

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Basic information

Entry
Database: PDB / ID: 4pdw
TitleA benzonitrile analogue inhibits rhinovirus replication
Components
  • (Genome polyprotein) x 3
  • Capsid protein VP4/VP2
KeywordsVIRUS / benzonitrile inhibitor
Function / homology
Function and homology information


lysis of host organelle 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / host cell ...lysis of host organelle 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / 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
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Picornavirus coat protein VP4 superfamily / 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 coat protein VP4 / Rhinovirus 14, subunit 4 / Picornavirus coat protein VP4 superfamily / 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) / 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 / Few Secondary Structures / Irregular / 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
Chem-2XK / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 14
Rhinovirus B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsQuerol-Audi, J. / Guerra, P. / Lacroix, C. / Roche, M. / Franco, D. / Froeyen, M. / Terme, T. / Vanelle, P. / Neyts, J. / Leyssen, P. / Verdaguer, N.
CitationJournal: J.Antimicrob.Chemother. / Year: 2014
Title: A novel benzonitrile analogue inhibits rhinovirus replication.
Authors: Lacroix, C. / Querol-Audi, J. / Roche, M. / Franco, D. / Froeyen, M. / Guerra, P. / Terme, T. / Vanelle, P. / Verdaguer, N. / Neyts, J. / Leyssen, P.
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Dec 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Capsid protein VP4/VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1779
Polymers94,4834
Non-polymers6955
Water1,24369
1
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Capsid protein VP4/VP2
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,710,632540
Polymers5,668,952240
Non-polymers41,681300
Water4,324240
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: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Capsid protein VP4/VP2
hetero molecules
x 5


  • icosahedral pentamer
  • 476 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)475,88645
Polymers472,41320
Non-polymers3,47325
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Genome polyprotein
B: Genome polyprotein
C: Genome polyprotein
D: Capsid protein VP4/VP2
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 571 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)571,06354
Polymers566,89524
Non-polymers4,16830
Water43224
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)439.411, 439.411, 439.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.84218, 0.46711, -0.26934), (-0.44077, 0.30867, -0.84288), (-0.31058, 0.82857, 0.46585)-38.809, 120.256, -66.039
3generate(0.58815, 0.31582, -0.74454), (-0.24378, -0.80855, -0.53555), (-0.77113, 0.49649, -0.39856)2.126, 230.147, 14.957
4generate(0.58803, -0.24431, -0.77106), (0.31676, -0.80759, 0.49746), (-0.74423, -0.53676, -0.39749)66.339, 177.836, 130.938
5generate(0.84366, -0.43819, -0.31022), (0.46597, 0.31061, 0.82849), (-0.26668, -0.84351, 0.46623)64.825, 35.539, 121.663
6generate(-0.7043, -0.62811, -0.33081), (-0.62649, 0.33078, 0.70575), (-0.33387, 0.70431, -0.62648)-82.23, -73.134, 65.351
7generate(-0.21585, -0.79763, 0.56321), (-0.8931, 0.39444, 0.21633), (-0.3947, -0.4563, -0.7975)-108.41, -55.568, 204.286
8generate(-0.00683, 0.11948, 0.99281), (-0.99319, -0.11629, 0.00716), (0.11631, -0.986, 0.11946)-233.13, 12.328, 217.397
9generate(-0.36713, 0.85632, 0.36322), (-0.78891, -0.49353, 0.36613), (0.49278, -0.15213, 0.85675)-284.056, 36.534, 86.515
10generate(-0.79853, 0.39325, -0.45574), (-0.56277, -0.21903, 0.79707), (0.21363, 0.89296, 0.39621)-190.6, -16.013, -7.521
11generate(0.85809, -0.4902, -0.15295), (-0.36156, -0.36525, -0.85783), (0.36465, 0.79139, -0.49065)54.737, 204.172, 117.498
12generate(0.986, 0.12174, 0.11392), (0.12183, -0.99253, 0.00614), (0.11382, 0.00782, -0.99347)-27.412, 230.926, 230.914
13generate(0.7422, 0.59226, -0.31365), (0.53655, -0.2447, 0.80761), (0.40156, -0.76769, -0.4994)-58.639, 106.437, 293.051
14generate(0.46501, 0.27058, -0.84294), (0.30621, 0.84422, 0.43991), (0.83066, -0.46268, 0.30972)4.178, 2.789, 217.867
15generate(0.53738, -0.39697, -0.74407), (-0.2474, 0.76927, -0.58908), (0.80624, 0.50064, 0.31518)74.082, 63.181, 109.391
16generate(-0.50027, 0.31028, 0.80837), (-0.40214, 0.74354, -0.53426), (-0.76682, -0.59235, -0.24719)-287.694, 43.011, 117.576
17generate(-0.80955, 0.53283, 0.24642), (-0.49788, -0.40077, -0.76909), (-0.31104, -0.7453, 0.58973)-284.343, 183.369, 92.385
18generate(-0.99264, -0.00727, -0.12086), (-0.00644, -0.99361, 0.11268), (-0.12091, 0.11263, 0.98625)-205.177, 205.391, -23.959
19generate(-0.79569, -0.56603, 0.21564), (0.3956, -0.21604, 0.89265), (-0.45868, 0.79558, 0.39582)-159.43, 78.629, -70.791
20generate(-0.49164, -0.36853, 0.78897), (0.14877, 0.85716, 0.49309), (-0.858, 0.3598, -0.36659)-210.495, -21.654, 16.712

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Genome polyprotein


Mass: 32560.549 Da / Num. of mol.: 1 / Fragment: resdiues 568-856 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14
References: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein Genome polyprotein


Mass: 28501.361 Da / Num. of mol.: 1 / Fragment: resdiues 70-331 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14
References: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein Genome polyprotein


Mass: 26236.754 Da / Num. of mol.: 1 / Fragment: resdiues 332-657 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14
References: UniProt: P03303, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein Capsid protein VP4/VP2


Mass: 7183.863 Da / Num. of mol.: 1 / Fragment: residue 2-69 / Source method: isolated from a natural source / Source: (natural) Rhinovirus B / References: UniProt: F5A5A0

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Non-polymers , 3 types, 74 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-2XK / 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile


Mass: 326.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14N2O5
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: PEG 8000, calcium chloride

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 3→49.75 Å / Num. obs: 553702 / % possible obs: 99.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.203 / Rsym value: 0.233 / Net I/σ(I): 6.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.3 / Num. unique all: 80647 / % possible all: 99.5

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Processing

Software
NameClassification
XDSdata reduction
MOLREPphasing
SCALAdata scaling
CNSrefinement
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HRV

1hrv


Resolution: 3→49.75 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2 27658 5 %random selection
Rwork0.2 ---
obs-553620 99.4 %-
Refinement stepCycle: LAST / Resolution: 3→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6241 0 48 69 6358

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