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- PDB-1po2: POLIOVIRUS (TYPE 1, MAHONEY) IN COMPLEX WITH R77975, AN INHIBITOR... -

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Basic information

Entry
Database: PDB / ID: 1po2
TitlePOLIOVIRUS (TYPE 1, MAHONEY) IN COMPLEX WITH R77975, AN INHIBITOR OF VIRAL REPLICATION
Components(POLIOVIRUS TYPE 1 ...) x 5
KeywordsVIRUS / POLIOVIRUS / PICORNAVIRUS COAT PROTEIN / ANTI-VIRAL DRUGS / HYDROLASE / THIOL PROTEASE / Icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase 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 ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase 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 / symbiont-mediated suppression of host gene expression / 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 / RNA-directed 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
Picornavirus coat protein VP4 / 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 / 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) / 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. / 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-J77 / MYRISTIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHiremath, C.N. / Filman, D.J. / Grant, R.A. / Hogle, J.M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Ligand-induced conformational changes in poliovirus-antiviral drug complexes.
Authors: Hiremath, C.N. / Filman, D.J. / Grant, R.A. / Hogle, J.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Binding of the Antiviral Drug Win51711 to the Sabin Strain of Type 3 Poliovirus: Structural Comparison with Drug Binding in Rhinovirus 14
Authors: Hiremath, C.N. / Grant, R.A. / Filman, D.J. / Hogle, J.M.
#2: Journal: Curr.Biol. / Year: 1994
Title: Structures of Poliovirus Complexes with Anti-Viral Drugs: Implications for Viral Stability and Drug Design
Authors: Grant, R.A. / Hiremath, C.N. / Filman, D.J. / Syed, R. / Andries, K. / Hogle, J.M.
#3: Journal: New Aspects of Positive-Strand RNA Viruses / Year: 1990
Title: Role of Conformational Transitions in Poliovirus Assembly and Cell Entry
Authors: Hogle, J.M. / Syed, R. / Fricks, C.E. / Icenogle, J.P. / Flore, O. / Filman, D.J.
#4: Journal: Embo J. / Year: 1989
Title: Structural Factors that Control Conformational Transitions and Serotype Specificity in Type 3 Poliovirus
Authors: Filman, D.J. / Syed, R. / Chow, M. / Macadam, A.J. / Minor, P.D. / Hogle, J.M.
#5: Journal: Nature / Year: 1987
Title: Myristylation of Picornavirus Capsid Protein Vp4 and its Structural Significance
Authors: Chow, M. / Newman, J.F. / Filman, D. / Hogle, J.M. / Rowlands, D.J. / Brown, F.
#6: Journal: Science / Year: 1985
Title: Three-Dimensional Structure of Poliovirus at 2.9 A Resolution
Authors: Hogle, J.M. / Chow, M. / Filman, D.J.
#7: Journal: Nucleic Acids Res. / Year: 1983
Title: The Nucleotide Sequence of Poliovirus Type 3 Leon 12 A1B: Comparison with Poliovirus Type 1
Authors: Stanway, G. / Cann, A.J. / Hauptmann, R. / Hughes, P. / Clarke, L.D. / Mountford, R.C. / Minor, P.D. / Schild, G.C. / Almond, J.W.
History
DepositionJan 8, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_ref_seq_dif / struct_site
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_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][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_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: POLIOVIRUS TYPE 1 MAHONEY
1: POLIOVIRUS TYPE 1 MAHONEY
2: POLIOVIRUS TYPE 1 MAHONEY
3: POLIOVIRUS TYPE 1 MAHONEY
4: POLIOVIRUS TYPE 1 MAHONEY
1: (METHYLPYRIDAZINE PIPERIDINE ETHYLOXYPHENYL)ETHYLACETATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5407
Polymers97,9425
Non-polymers5982
Water00
1
0: POLIOVIRUS TYPE 1 MAHONEY
1: POLIOVIRUS TYPE 1 MAHONEY
2: POLIOVIRUS TYPE 1 MAHONEY
3: POLIOVIRUS TYPE 1 MAHONEY
4: POLIOVIRUS TYPE 1 MAHONEY
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,912,410420
Polymers5,876,540300
Non-polymers35,870120
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
0: POLIOVIRUS TYPE 1 MAHONEY
1: POLIOVIRUS TYPE 1 MAHONEY
2: POLIOVIRUS TYPE 1 MAHONEY
3: POLIOVIRUS TYPE 1 MAHONEY
4: POLIOVIRUS TYPE 1 MAHONEY
hetero molecules
x 5


  • icosahedral pentamer
  • 493 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)492,70135
Polymers489,71225
Non-polymers2,98910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
0: POLIOVIRUS TYPE 1 MAHONEY
1: POLIOVIRUS TYPE 1 MAHONEY
2: POLIOVIRUS TYPE 1 MAHONEY
3: POLIOVIRUS TYPE 1 MAHONEY
4: POLIOVIRUS TYPE 1 MAHONEY
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 591 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)591,24142
Polymers587,65430
Non-polymers3,58712
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
0: POLIOVIRUS TYPE 1 MAHONEY
1: POLIOVIRUS TYPE 1 MAHONEY
2: POLIOVIRUS TYPE 1 MAHONEY
3: POLIOVIRUS TYPE 1 MAHONEY
4: POLIOVIRUS TYPE 1 MAHONEY
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.96 MDa, 150 polymers
Theoretical massNumber of molelcules
Total (without water)2,956,205210
Polymers2,938,270150
Non-polymers17,93560
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)322.940, 358.040, 380.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30930465, -0.81642343, 0.48763205), (0.80161055, 0.49971234, 0.32819023), (-0.51161448, 0.28937827, 0.80901699)46.3008, 31.16175, -18.13389
3generate(-0.80826389, -0.51939032, 0.27738728), (0.48060969, -0.30977009, 0.82040318), (-0.34018087, 0.79641188, 0.5)26.338, 77.89751, -47.47514
4generate(-0.80826389, 0.48060968, -0.34018318), (-0.51939032, -0.3097701, 0.79641728), (0.2773854, 0.82039762, 0.5)-32.30049, 75.62004, -47.47514
5generate(0.30930465, 0.80161055, -0.51161795), (-0.81642344, 0.49971234, 0.28938023), (0.48762875, 0.32818801, 0.80901699)-48.57827, 27.47673, -18.13389
6generate(-0.99698759, -0.07756126), (-0.07756126, 0.99698759), (-1)-189.90056
7generate(-0.37054682, 0.77520571, -0.51161795), (0.77520571, 0.56152983, 0.28938023), (0.51161448, -0.28937827, -0.80901699)-48.57827, 27.47673, -171.76667
8generate(0.76855237, 0.54185186, -0.34018318), (0.54185186, -0.26855237, 0.79641728), (0.34018087, -0.79641188, -0.5)-32.30049, 75.62004, -142.42542
9generate(0.84611363, -0.45513573, 0.27738728), (-0.45513573, -0.34611363, 0.82040318), (-0.2773854, -0.82039762, -0.5)26.338, 77.89751, -142.42542
10generate(-0.24505007, -0.83795409, 0.48763205), (-0.83795409, 0.43603308, 0.32819023), (-0.48762875, -0.32818801, -0.80901699)46.3008, 31.16175, -171.76667
11generate(-0.03878063, -0.00150621, 0.99925), (0.9984938, 0.03878063, 0.03881), (-0.03880974, 0.99924323)94.87907, 3.68502, -94.95028
12generate(-0.52443319, 0.32006998, 0.78900523), (0.32006998, -0.7845838, 0.53102295), (0.78899988, 0.53101935, 0.30901699)74.91627, 50.42078, -65.60903
13generate(-0.30930465, 0.81642343, 0.48763205), (-0.80161055, -0.49971234, 0.32819023), (0.51161448, -0.28937827, 0.80901699)46.3008, 31.16175, -18.13389
14generate(0.30930465, 0.80161055, 0.51161795), (-0.81642344, 0.49971234, -0.28938023), (-0.48762875, -0.32818801, 0.80901699)48.57827, -27.47673, -18.13389
15generate(0.4764977, 0.29610223, 0.82781523), (0.29610223, 0.8325193, -0.46822705), (-0.82780962, 0.46822388, 0.30901699)78.60129, -44.45829, -65.60903
16generate(0.03878063, 0.00150621, 0.99925), (-0.9984938, -0.03878063, 0.03881), (0.03880974, -0.99924323)94.87907, 3.68502, -94.95028
17generate(-0.49802835, 0.25825249, 0.82781523), (-0.3597815, 0.80704534, -0.46822705), (-0.78899988, -0.53101935, -0.30901699)78.60129, -44.45829, -124.29153
18generate(-0.37054682, 0.77520571, 0.51161795), (0.77520571, 0.56152983, -0.28938023), (-0.51161448, 0.28937827, -0.80901699)48.57827, -27.47673, -171.76667
19generate(0.24505007, 0.83795409, 0.48763205), (0.83795409, -0.43603308, 0.32819023), (0.48762875, 0.32818801, -0.80901699)46.3008, 31.16175, -171.76667
20generate(0.49802835, 0.3597815, 0.78900523), (-0.25825249, -0.80704534, 0.53102295), (0.82780962, -0.46822388, -0.30901699)74.91627, 50.42078, -124.29153
21generate(-0.03878063, 0.9984938, -0.03881), (-0.00150621, 0.03878063, 0.99925), (0.99924323, 0.03880974)-3.68502, 94.87907, -94.95028
22generate(0.80826389, 0.51939032, 0.27738728), (-0.48060969, 0.30977009, 0.82040318), (0.34018087, -0.79641188, 0.5)26.338, 77.89751, -47.47514
23generate(0.52443319, -0.32006998, 0.78900523), (-0.32006998, 0.7845838, 0.53102295), (-0.78899988, -0.53101935, 0.30901699)74.91627, 50.42078, -65.60903
24generate(-0.49802835, -0.3597815, 0.78900523), (0.25825249, 0.80704534, 0.53102295), (-0.82780962, 0.46822388, -0.30901699)74.91627, 50.42078, -124.29153
25generate(-0.84611363, 0.45513573, 0.27738728), (0.45513573, 0.34611363, 0.82040318), (0.2773854, 0.82039762, -0.5)26.338, 77.89751, -142.42542
26generate(0.03878063, -0.9984938, -0.03881), (0.00150621, -0.03878063, 0.99925), (-0.99924323, -0.03880974)-3.68502, 94.87907, -94.95028
27generate(-0.76855237, -0.54185186, -0.34018318), (-0.54185186, 0.26855237, 0.79641728), (-0.34018087, 0.79641188, -0.5)-32.30049, 75.62004, -142.42542
28generate(-0.49802835, 0.25825249, -0.82781523), (-0.3597815, 0.80704534, 0.46822705), (0.78899988, 0.53101935, -0.30901699)-78.60129, 44.45829, -124.29153
29generate(0.4764977, 0.29610223, -0.82781523), (0.29610223, 0.8325193, 0.46822705), (0.82780962, -0.46822388, 0.30901699)-78.60129, 44.45829, -65.60903
30generate(0.80826389, -0.48060968, -0.34018318), (0.51939032, 0.3097701, 0.79641728), (-0.2773854, -0.82039762, 0.5)-32.30049, 75.62004, -47.47514

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Components

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POLIOVIRUS TYPE 1 ... , 5 types, 5 molecules 01234

#1: Protein/peptide POLIOVIRUS TYPE 1 MAHONEY / P1/MAHONEY


Mass: 437.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: P1/MAHONEY PREPARED FROM A LOW-PASSAGE STOCK, PROVIDED BY MARIE CHOW, OF A PLAQUE ISOLATED FROM HELA CELLS TRANSFECTED WITH AN INFECTIOUS CDNA CLONE OF THE VIRAL GENOME. THE ANTIVIRAL ...Details: P1/MAHONEY PREPARED FROM A LOW-PASSAGE STOCK, PROVIDED BY MARIE CHOW, OF A PLAQUE ISOLATED FROM HELA CELLS TRANSFECTED WITH AN INFECTIOUS CDNA CLONE OF THE VIRAL GENOME. THE ANTIVIRAL COMPOUND R77975 WAS DEVELOPED BY JANSSEN PHARMACEUTICA.
Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney
#2: Protein POLIOVIRUS TYPE 1 MAHONEY / P1/MAHONEY


Mass: 33488.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: P1/MAHONEY PREPARED FROM A LOW-PASSAGE STOCK, PROVIDED BY MARIE CHOW, OF A PLAQUE ISOLATED FROM HELA CELLS TRANSFECTED WITH AN INFECTIOUS CDNA CLONE OF THE VIRAL GENOME. THE ANTIVIRAL ...Details: P1/MAHONEY PREPARED FROM A LOW-PASSAGE STOCK, PROVIDED BY MARIE CHOW, OF A PLAQUE ISOLATED FROM HELA CELLS TRANSFECTED WITH AN INFECTIOUS CDNA CLONE OF THE VIRAL GENOME. THE ANTIVIRAL COMPOUND R77975 WAS DEVELOPED BY JANSSEN PHARMACEUTICA.
Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Cell line: HELA / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#3: Protein POLIOVIRUS TYPE 1 MAHONEY / P1/MAHONEY


Mass: 30075.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: P1/MAHONEY PREPARED FROM A LOW-PASSAGE STOCK, PROVIDED BY MARIE CHOW, OF A PLAQUE ISOLATED FROM HELA CELLS TRANSFECTED WITH AN INFECTIOUS CDNA CLONE OF THE VIRAL GENOME. THE ANTIVIRAL ...Details: P1/MAHONEY PREPARED FROM A LOW-PASSAGE STOCK, PROVIDED BY MARIE CHOW, OF A PLAQUE ISOLATED FROM HELA CELLS TRANSFECTED WITH AN INFECTIOUS CDNA CLONE OF THE VIRAL GENOME. THE ANTIVIRAL COMPOUND R77975 WAS DEVELOPED BY JANSSEN PHARMACEUTICA.
Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Cell line: HELA / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#4: Protein POLIOVIRUS TYPE 1 MAHONEY / P1/MAHONEY


Mass: 26547.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: P1/MAHONEY PREPARED FROM A LOW-PASSAGE STOCK, PROVIDED BY MARIE CHOW, OF A PLAQUE ISOLATED FROM HELA CELLS TRANSFECTED WITH AN INFECTIOUS CDNA CLONE OF THE VIRAL GENOME. THE ANTIVIRAL ...Details: P1/MAHONEY PREPARED FROM A LOW-PASSAGE STOCK, PROVIDED BY MARIE CHOW, OF A PLAQUE ISOLATED FROM HELA CELLS TRANSFECTED WITH AN INFECTIOUS CDNA CLONE OF THE VIRAL GENOME. THE ANTIVIRAL COMPOUND R77975 WAS DEVELOPED BY JANSSEN PHARMACEUTICA.
Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Cell line: HELA / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#5: Protein POLIOVIRUS TYPE 1 MAHONEY / P1/MAHONEY


Mass: 7393.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: P1/MAHONEY PREPARED FROM A LOW-PASSAGE STOCK, PROVIDED BY MARIE CHOW, OF A PLAQUE ISOLATED FROM HELA CELLS TRANSFECTED WITH AN INFECTIOUS CDNA CLONE OF THE VIRAL GENOME. THE ANTIVIRAL ...Details: P1/MAHONEY PREPARED FROM A LOW-PASSAGE STOCK, PROVIDED BY MARIE CHOW, OF A PLAQUE ISOLATED FROM HELA CELLS TRANSFECTED WITH AN INFECTIOUS CDNA CLONE OF THE VIRAL GENOME. THE ANTIVIRAL COMPOUND R77975 WAS DEVELOPED BY JANSSEN PHARMACEUTICA.
Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Cell line: HELA / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300*PLUS

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Non-polymers , 2 types, 2 molecules 1

#6: Chemical ChemComp-J77 / (METHYLPYRIDAZINE PIPERIDINE ETHYLOXYPHENYL)ETHYLACETATE / R77975


Mass: 369.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N3O3
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 30 %
Crystal growpH: 7 / Details: pH 7.
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 %(v/v)ethylene glycol11
210 mMNaPIPES11
35 mM11MgCl2
41 mM11CaCl2

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Data collection

DiffractionMean temperature: 261 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorDate: 1995 / Details: FRANKS MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.9 Å / Num. obs: 306408 / % possible obs: 24 % / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.148
Reflection
*PLUS
Num. measured all: 587697

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REFINED STRUCTURE OF P1/MAHONEY (2PLV), AFTER OMITTING ALL LIGANDS, SOLVENT, AND ANY AMINO ACID LOCATED CLOSE TO A SIGNIFICANT ELECTRON DENSITY FEATURE IN THE NON-CRYSTALLOGRAPHIC ...Starting model: REFINED STRUCTURE OF P1/MAHONEY (2PLV), AFTER OMITTING ALL LIGANDS, SOLVENT, AND ANY AMINO ACID LOCATED CLOSE TO A SIGNIFICANT ELECTRON DENSITY FEATURE IN THE NON-CRYSTALLOGRAPHIC SYMMETRY-AVERAGED DIFFERENCE MAP.

2plv


Rfactor Rwork: 0.249 / Highest resolution: 2.9 Å
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6646 0 42 0 6688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.5
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: 'PSEUDO-CELL BASED APPROACH' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_dihedral_angle_deg / Dev ideal: 26

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