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- PDB-1ruc: RHINOVIRUS 14 MUTANT N1105S COMPLEXED WITH ANTIVIRAL COMPOUND WIN... -

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Basic information

Entry
Database: PDB / ID: 1ruc
TitleRHINOVIRUS 14 MUTANT N1105S COMPLEXED WITH ANTIVIRAL COMPOUND WIN 52035
Components(RHINOVIRUS 14) x 4
KeywordsVIRUS / RHINOVIRUS COAT PROTEIN / Icosahedral virus
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 / nucleoside-triphosphate phosphatase / channel activity ...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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase activity / DNA-templated transcription / : / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
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-W35 / Genome polyprotein
Similarity search - Component
Biological speciesHuman rhinovirus 14
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsHadfield, A. / Oliveira, M.A. / Kim, K.H. / Minor, I. / Kremer, M.J. / Heinz, B.A. / Shepard, D. / Pevear, D.C. / Rueckert, R.R. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Structural studies on human rhinovirus 14 drug-resistant compensation mutants.
Authors: Hadfield, A.T. / Oliveira, M.A. / Kim, K.H. / Minor, I. / Kremer, M.J. / Heinz, B.A. / Shepard, D. / Pevear, D.C. / Rueckert, R.R. / Rossmann, M.G.
#1: Journal: J.Virol. / Year: 1993
Title: Win 52035-2 Inhibits Both Attachment and Eclipse of Human Rhinovirus 14
Authors: Shepard, D.A. / Heinz, B.A. / Rueckert, R.R.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Analysis of the Structure of a Common Cold Virus, Human Rhinovirus 14, Refined at a Resolution of 3.0 Angstroms
Authors: Arnold, E. / Rossmann, M.G.
#3: Journal: J.Mol.Biol. / Year: 1989
Title: Three Dimensional Structures of Drug-Resistant Mutants of Human Rhinovirus 14
Authors: Badger, J. / Krishnaswamy, S. / Kremer, M.J. / Oliveira, M.A. / Rossmann, M.G. / Heinz, B.A. / Rueckert, R.R. / Dutko, F.J. / Mckinlay, M.A.
#4: Journal: Proteins / Year: 1989
Title: Structural Analysis of Antiviral Agents that Interact with the Capsid of Human Rhinoviruses
Authors: Badger, J. / Minor, I. / Oliveira, M.A. / Smith, T.J. / Rossmann, M.G.
#5: Journal: J.Virol. / Year: 1989
Title: Genetics and Molecular Basis for Resistance of Human Rhinovirus 14 to an Antiviral Drug
Authors: Heinz, B.A. / Rueckert, R.R. / Shepard, D.A. / Dutko, F.J. / Mckinlay, M.A. / Fancher, M. / Rossmann, M.G. / Badger, J. / Smith, T.J.
#6: Journal: Acta Crystallogr.,Sect.A / Year: 1988
Title: The Use of Molecular Replacement Phases for the Refinement of the Human Rhinovirus 14 Structure
Authors: Arnold, E. / Rossmann, M.G.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Structural Analysis of a Series of Antiviral Agents Complexed with Human Rhinovirus 14
Authors: Badger, J. / Minor, I. / Kremer, M.J. / Oliveira, M.A. / Smith, T.J. / Griffith, J.P. / Guerin, D.M.A. / Krishnaswamy, S. / Luo, M. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Dutko, F. ...Authors: Badger, J. / Minor, I. / Kremer, M.J. / Oliveira, M.A. / Smith, T.J. / Griffith, J.P. / Guerin, D.M.A. / Krishnaswamy, S. / Luo, M. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Dutko, F.J. / Fancher, M. / Rueckert, R.R. / Heinz, B.A.
#8: Journal: Acta Crystallogr.,Sect.A / Year: 1987
Title: The Structure Determination of a Common Cold Virus, Human Rhinovirus 14
Authors: Arnold, E. / Vriend, G. / Luo, M. / Griffith, J.P. / Kamer, G. / Erickson, J.W. / Johnson, J.E. / Rossmann, M.G.
#9: Journal: Science / Year: 1986
Title: The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating
Authors: Smith, T.J. / Kremer, M.J. / Luo, M. / Vriend, G. / Arnold, E. / Kamer, G. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Otto, M.J.
#10: Journal: Nature / Year: 1985
Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.-J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / Rueckert, R.R. / Sherry, B. / Vriend, G.
#11: Journal: J.Mol.Biol. / Year: 1984
Title: Virion Orientation in Cubic Crystals of the Human Common Cold Virus Hrv14
Authors: Arnold, E. / Erickson, J.W. / Fout, G.S. / Frankenberger, E.A. / Hecht, H.-J. / Luo, M. / Rossmann, M.G. / Rueckert, R.R.
History
DepositionJun 9, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_radiation_wavelength ...database_2 / diffrn_radiation_wavelength / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jan 18, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 700SHEET THERE IS A BIFURCATED SHEET IN EACH OF CHAINS *1*, *2*, AND *3*. TO REPRESENT THIS FEATURE ...SHEET THERE IS A BIFURCATED SHEET IN EACH OF CHAINS *1*, *2*, AND *3*. TO REPRESENT THIS FEATURE REDUNDANT SHEETS ARE DEFINED. THUS SHEETS B11 AND B12 DIFFER ONLY IN STRAND 4, SHEETS B12 AND B22 DIFFER ONLY IN STRAND 4, AND SHEETS B13 AND B23 DIFFER IN STRANDS 1 AND 4 (DOUBLY BIFURCATED).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: RHINOVIRUS 14
2: RHINOVIRUS 14
3: RHINOVIRUS 14
4: RHINOVIRUS 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7705
Polymers94,4564
Non-polymers3141
Water00
1
1: RHINOVIRUS 14
2: RHINOVIRUS 14
3: RHINOVIRUS 14
4: RHINOVIRUS 14
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,686,193300
Polymers5,667,330240
Non-polymers18,86360
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
1: RHINOVIRUS 14
2: RHINOVIRUS 14
3: RHINOVIRUS 14
4: RHINOVIRUS 14
hetero molecules
x 5


  • icosahedral pentamer
  • 474 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)473,84925
Polymers472,27820
Non-polymers1,5725
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: RHINOVIRUS 14
2: RHINOVIRUS 14
3: RHINOVIRUS 14
4: RHINOVIRUS 14
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 569 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)568,61930
Polymers566,73324
Non-polymers1,8866
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
1: RHINOVIRUS 14
2: RHINOVIRUS 14
3: RHINOVIRUS 14
4: RHINOVIRUS 14
hetero molecules
x 20


  • crystal asymmetric unit, crystal frame
  • 1.9 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,895,398100
Polymers1,889,11080
Non-polymers6,28820
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation19
Unit cell
Length a, b, c (Å)445.100, 445.100, 445.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Atom site foot note1: CIS PROLINE - PRO 2 83
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.46428249, -0.82990465, 0.30935523), (0.84439659, 0.30935523, -0.43737202), (0.26727602, 0.46428249, 0.84439659)0.18336, 0.04923, -0.09998
3generate(-0.40252706, -0.49841714, 0.7678235), (0.53635794, -0.80813188, -0.2434001), (0.74181712, 0.31385302, 0.5926246)0.1967, 0.26302, -0.11254
4generate(-0.40252706, 0.53635794, 0.74181712), (-0.49841714, -0.80813188, 0.31385302), (0.7678235, -0.2434001, 0.5926246)0.02159, 0.34591, -0.02032
5generate(0.46428249, 0.84439659, 0.26727602), (-0.82990465, 0.30935523, 0.46428249), (0.30935523, -0.43737202, 0.84439659)-0.09998, 0.18336, 0.04923
6generate(-0.6305654, -0.70150875, 0.33207415), (-0.70150875, 0.33207415, -0.6305654), (0.33207415, -0.6305654, -0.70150875)0.34718, 0.34718, 0.34718
7generate(-0.79635651, 0.46046981, 0.39215364), (-0.21383107, 0.39215364, -0.89470238), (-0.56576752, -0.79635651, -0.21383107)0.16382, 0.29795, 0.44716
8generate(0.12389799, 0.98541842, -0.11662042), (-0.00727745, -0.11662042, -0.99315013), (-0.99226854, 0.12389799, -0.00727745)0.00127, 0.3675, 0.32559
9generate(0.85843766, 0.14787594, -0.49113956), (-0.36729797, -0.49113956, -0.7898572), (-0.35801899, 0.85843766, -0.36729797)0.08416, 0.45972, 0.15048
10generate(0.39215364, -0.89470238, -0.21383107), (-0.79635651, -0.21383107, -0.56576752), (0.46046981, 0.39215364, -0.79635651)0.29795, 0.44716, 0.16382
11generate(-0.49113956, -0.7898572, -0.36729797), (0.85843766, -0.36729797, -0.35801899), (0.14787594, -0.49113956, 0.85843766)0.45972, 0.15048, 0.08416
12generate(-0.99315013, -0.00727745, -0.11662042), (-0.00727745, -0.99226854, 0.12389799), (-0.11662042, 0.12389799, 0.98541842)0.3675, 0.32559, 0.00127
13generate(-0.49841714, 0.7678235, -0.40252706), (-0.80813188, -0.2434001, 0.53635794), (0.31385302, 0.5926246, 0.74181712)0.1967, 0.26302, -0.11254
14generate(0.30935523, 0.46428249, -0.82990465), (-0.43737202, 0.84439659, 0.30935523), (0.84439659, 0.26727602, 0.46428249)0.18336, 0.04923, -0.09998
15generate(0.31385302, -0.49841714, -0.80813188), (0.5926246, 0.7678235, -0.2434001), (0.74181712, -0.40252706, 0.53635794)0.34591, -0.02032, 0.02159
16generate(-0.2434001, 0.5926246, 0.7678235), (0.53635794, 0.74181712, -0.40252706), (-0.80813188, 0.31385302, -0.49841714)-0.02032, 0.02159, 0.34591
17generate(0.5926246, 0.74181712, 0.31385302), (0.7678235, -0.40252706, -0.49841714), (-0.2434001, 0.53635794, -0.80813188)-0.11254, 0.1967, 0.26302
18generate(0.98541842, -0.11662042, 0.12389799), (-0.11662042, -0.99315013, -0.00727745), (0.12389799, -0.00727745, -0.99226854)0.00127, 0.3675, 0.32559
19generate(0.39215364, -0.79635651, 0.46046981), (-0.89470238, -0.21383107, 0.39215364), (-0.21383107, -0.56576752, -0.79635651)0.16382, 0.29795, 0.44716
20generate(-0.36729797, -0.35801899, 0.85843766), (-0.49113956, 0.85843766, 0.14787594), (-0.7898572, -0.36729797, -0.49113956)0.15048, 0.08416, 0.45972

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Components

#1: Protein RHINOVIRUS 14 / HRV14


Mass: 32533.525 Da / Num. of mol.: 1 / Mutation: N(1)105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B
Description: HELA CELLS, MUTANTS FOUND BY SCREENING TECHNIQUES IN THE PRESENCE OF WIN COMPOUNDS WIN 52035 AND WIN 52084
Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303
#2: Protein RHINOVIRUS 14 / HRV14


Mass: 28501.361 Da / Num. of mol.: 1 / Mutation: N(1)105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B
Description: HELA CELLS, MUTANTS FOUND BY SCREENING TECHNIQUES IN THE PRESENCE OF WIN COMPOUNDS WIN 52035 AND WIN 52084
Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303
#3: Protein RHINOVIRUS 14 / HRV14


Mass: 26236.754 Da / Num. of mol.: 1 / Mutation: N(1)105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B
Description: HELA CELLS, MUTANTS FOUND BY SCREENING TECHNIQUES IN THE PRESENCE OF WIN COMPOUNDS WIN 52035 AND WIN 52084
Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303
#4: Protein RHINOVIRUS 14 / HRV14


Mass: 7183.863 Da / Num. of mol.: 1 / Mutation: N(1)105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B
Description: HELA CELLS, MUTANTS FOUND BY SCREENING TECHNIQUES IN THE PRESENCE OF WIN COMPOUNDS WIN 52035 AND WIN 52084
Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P03303
#5: Chemical ChemComp-W35 / 5-(5-(4-(4,5-DIHYDRO-2-OXAZOLY)PHENOXY)PENTYL)-3-METHYL ISOXAZOLE / WIN VI / WIN 52035


Mass: 314.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N2O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlvirus1drop
20.125 %(w/v)PEG80001dropor 0.25 %(w/v)
30.01 MTris-HCl1drop
40.25 %(w/v)PEG80001reservoiror 0.5 %(w/v)
50.02 M1reservoirCaCl2
60.01 MTris-HCl1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.563 Å
DetectorType: KODAK / Detector: FILM / Date: Apr 1, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.563 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 89386 / % possible obs: 18 % / Observed criterion σ(I): 3.5 / Rmerge(I) obs: 0.104
Reflection
*PLUS
Num. measured all: 102231

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Processing

Software
NameVersionClassification
Omodel building
PURDUEDATA PROCESSING PACKAGEdata reduction
RefinementHighest resolution: 3.1 Å
Details: CONFORMATIONAL DIFFERENCES OCCUR IN THE RESIDUES EITHER SIDE OF SER 1 105 AND ASN 1 219 IN CHAIN 1 AT THE DRUG BINDING SITE AND AROUND ASN 1 141 IN CHAIN 1 AT THE ICOSAHEDRAL FIVE-FOLD AXIS.
Refinement stepCycle: LAST / Highest resolution: 3.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 23 0 6289

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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