[English] 日本語
Yorodumi
- PDB-1po2: POLIOVIRUS (TYPE 1, MAHONEY) IN COMPLEX WITH R77975, AN INHIBITOR... -

+
Open data


ID or keywords:

Loading...

-
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 MDA-5 activity / 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-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / 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 MDA-5 activity / 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-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / 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 / 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 / structural molecule activity / virion attachment to host cell / 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) / 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. / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
Components

-
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

-
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 / Myristic acid


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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

Read more