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- PDB-1piv: BINDING OF THE ANTIVIRAL DRUG WIN51711 TO THE SABIN STRAIN OF TYP... -

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Basic information

Entry
Database: PDB / ID: 1piv
TitleBINDING OF THE ANTIVIRAL DRUG WIN51711 TO THE SABIN STRAIN OF TYPE 3 POLIOVIRUS: STRUCTURAL COMPARISON WITH DRUG BINDING IN RHINOVIRUS 14
Components(POLIOVIRUS TYPE 3 (SUBUNIT ...) x 5
KeywordsVIRUS / Icosahedral virus
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / 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 / 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 ...caveolin-mediated endocytosis of virus by host cell / 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 / 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 / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / Chem-W71 / Genome polyprotein
Similarity search - Component
Biological speciesPoliovirus type 3
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsHiremath, C.N. / Grant, R.A. / Filman, D.J. / Hogle, J.M.
Citation
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.
#1: 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. / Hogle, J.M.
#2: 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.
#3: 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.
#4: Journal: Nucleic Acids Res. / Year: 1983
Title: The Nucleotide Sequence of Poliovirus Type 3 Leon 12A1B: Comparison with Poliovirus Type 1
Authors: Stanway, G. / Cann, A.J. / Hauptman, R. / Hughes, P. / Clarke, L.D. / Mountford, R.C. / Minor, P.D. / Schild, G.C. / Almond, J.W.
History
DepositionFeb 2, 1995-
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: POLIOVIRUS TYPE 3 (SUBUNIT VP1)
1: POLIOVIRUS TYPE 3 (SUBUNIT VP1)
2: POLIOVIRUS TYPE 3 (SUBUNIT VP2)
3: POLIOVIRUS TYPE 3 (SUBUNIT VP3)
4: POLIOVIRUS TYPE 3 (SUBUNIT VP4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4497
Polymers97,8785
Non-polymers5712
Water0
1
0: POLIOVIRUS TYPE 3 (SUBUNIT VP1)
1: POLIOVIRUS TYPE 3 (SUBUNIT VP1)
2: POLIOVIRUS TYPE 3 (SUBUNIT VP2)
3: POLIOVIRUS TYPE 3 (SUBUNIT VP3)
4: POLIOVIRUS TYPE 3 (SUBUNIT VP4)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,906,944420
Polymers5,872,696300
Non-polymers34,248120
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
0: POLIOVIRUS TYPE 3 (SUBUNIT VP1)
1: POLIOVIRUS TYPE 3 (SUBUNIT VP1)
2: POLIOVIRUS TYPE 3 (SUBUNIT VP2)
3: POLIOVIRUS TYPE 3 (SUBUNIT VP3)
4: POLIOVIRUS TYPE 3 (SUBUNIT VP4)
hetero molecules
x 5


  • icosahedral pentamer
  • 492 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)492,24535
Polymers489,39125
Non-polymers2,85410
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
0: POLIOVIRUS TYPE 3 (SUBUNIT VP1)
1: POLIOVIRUS TYPE 3 (SUBUNIT VP1)
2: POLIOVIRUS TYPE 3 (SUBUNIT VP2)
3: POLIOVIRUS TYPE 3 (SUBUNIT VP3)
4: POLIOVIRUS TYPE 3 (SUBUNIT VP4)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 591 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)590,69442
Polymers587,27030
Non-polymers3,42512
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
0: POLIOVIRUS TYPE 3 (SUBUNIT VP1)
1: POLIOVIRUS TYPE 3 (SUBUNIT VP1)
2: POLIOVIRUS TYPE 3 (SUBUNIT VP2)
3: POLIOVIRUS TYPE 3 (SUBUNIT VP3)
4: POLIOVIRUS TYPE 3 (SUBUNIT VP4)
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 1.48 MDa, 75 polymers
Theoretical massNumber of molelcules
Total (without water)1,476,736105
Polymers1,468,17475
Non-polymers8,56230
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation15
Unit cell
Length a, b, c (Å)321.060, 358.620, 381.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: CIS PROLINE - PRO 2 83
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)
4generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)
5generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)
6generate(1), (1), (1)
7generate(-0.5, 0.30901699, 0.80901699), (0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699)
8generate(-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699)
9generate(0.30901699, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699)
10generate(0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699)
11generate(1), (1), (1)
12generate(0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699), (0.30901699, -0.80901699, 0.5)
13generate(0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5), (-0.80901699, -0.5, 0.30901699)
14generate(-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5), (-0.80901699, 0.5, -0.30901699)
15generate(-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699), (0.30901699, 0.80901699, -0.5)

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Components

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POLIOVIRUS TYPE 3 (SUBUNIT ... , 5 types, 5 molecules 01234

#1: Protein/peptide POLIOVIRUS TYPE 3 (SUBUNIT VP1)


Mass: 446.495 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THIS ENTITY REPRESENTS A FEATURE IN THE ELECTRON DENSITY MAP WHICH APPEARS TO BE A BETA STRAND. ALTHOUGH THE SIDE CHAINS OF THIS STRAND CANNOT BE CORRELATED RELIABLY WITH THE SEQUENCE OF THE ...Details: THIS ENTITY REPRESENTS A FEATURE IN THE ELECTRON DENSITY MAP WHICH APPEARS TO BE A BETA STRAND. ALTHOUGH THE SIDE CHAINS OF THIS STRAND CANNOT BE CORRELATED RELIABLY WITH THE SEQUENCE OF THE PROTEIN, THE FEATURE IS BELIEVED LIKELY TO CORRESPOND TO SOME PORTION OF THE AMINO TERMINAL EXTENSION OF VP1.
Source: (gene. exp.) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B)
Genus: Enterovirus / Species: Poliovirus / Strain: 3-LEON-12A(1)B PLACQUE 411
#2: Protein POLIOVIRUS TYPE 3 (SUBUNIT VP1)


Mass: 33651.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B)
Genus: Enterovirus / Species: Poliovirus / Strain: 3-LEON-12A(1)B PLACQUE 411 / Organ: SEED / References: UniProt: P03302
#3: Protein POLIOVIRUS TYPE 3 (SUBUNIT VP2)


Mass: 30169.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B)
Genus: Enterovirus / Species: Poliovirus / Strain: 3-LEON-12A(1)B PLACQUE 411 / Organ: SEED / References: UniProt: P03302
#4: Protein POLIOVIRUS TYPE 3 (SUBUNIT VP3)


Mass: 26289.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B)
Genus: Enterovirus / Species: Poliovirus / Strain: 3-LEON-12A(1)B PLACQUE 411 / Organ: SEED / References: UniProt: P03302
#5: Protein POLIOVIRUS TYPE 3 (SUBUNIT VP4)


Mass: 7320.917 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B)
Genus: Enterovirus / Species: Poliovirus / Strain: 3-LEON-12A(1)B PLACQUE 411 / Organ: SEED / References: UniProt: P03302

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Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-W71 / 5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE / COMPOUND IV


Mass: 342.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N2O3
#7: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


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

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Details

Sequence detailsTHE APPROPRIATE SEQUENCE FOR THIS VIRUS CORRESPONDS TO THE STANWAY, ET AL. REFERENCE ABOVE.
Source detailsPOLIOVIRUS SEED STOCK OBTAINED FROM P. D. MINOR (NATIONAL INSTITUTE OF BIOLOGICAL STANDARDS AND ...POLIOVIRUS SEED STOCK OBTAINED FROM P. D. MINOR (NATIONAL INSTITUTE OF BIOLOGICAL STANDARDS AND CONTROL, LONDON)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: microdialysis / Details: Filman, D.J., (1989) Embo J., 8, 1567.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMPIPES11
25 mM11MgCl2
31 mM11CaCl2
40.5 M11NaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 121440 / % possible obs: 25 % / Observed criterion σ(F): 0
Reflection
*PLUS
Rmerge(I) obs: 0.166

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.316 / Highest resolution: 2.9 Å
Details: THE POLYPEPTIDE DESIGNATED IN THIS FILE AS RESIDUES 7 - 10 OF CHAIN 0 REPRESENTS A FEATURE IN THE ELECTRON DENSITY MAP WHICH APPEARS TO BE A BETA STRAND. ALTHOUGH THE SIDE CHAINS OF THIS ...Details: THE POLYPEPTIDE DESIGNATED IN THIS FILE AS RESIDUES 7 - 10 OF CHAIN 0 REPRESENTS A FEATURE IN THE ELECTRON DENSITY MAP WHICH APPEARS TO BE A BETA STRAND. ALTHOUGH THE SIDE CHAINS OF THIS STRAND CANNOT BE CORRELATED RELIABLY WITH THE SEQUENCE OF THE PROTEIN, THE FEATURE IS BELIEVED LIKELY TO CORRESPOND TO SOME PORTION OF THE AMINO TERMINAL EXTENSION OF VP1.
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6631 0 25 0 6656
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_deg2.6
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

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