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Yorodumi- PDB-1vbb: POLIOVIRUS (TYPE 3, SABIN STRAIN) (P3/SABIN, P3/LEON/12A(1)B) COM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vbb | ||||||
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Title | POLIOVIRUS (TYPE 3, SABIN STRAIN) (P3/SABIN, P3/LEON/12A(1)B) COMPLEXED WITH R80633 | ||||||
Components | (POLIOVIRUS TYPE ...) x 5 | ||||||
Keywords | VIRUS / VIRUS COAT PROTEIN / HYDROLASE / THIOL PROTEASE / 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 / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent 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 | ||||||
Biological species | Poliovirus type 3 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Grant, R.A. / Hiremath, C.N. / Filman, D.J. / Syed, R. / Andries, K. / Hogle, J.M. | ||||||
Citation | 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. #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: 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: 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. #5: Journal: Science / Year: 1985 Title: Three-Dimensional Structure of Poliovirus at 2.9 A Resolution Authors: Hogle, J.M. / Chow, M. / Filman, D.J. #6: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vbb.cif.gz | 174.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vbb.ent.gz | 136.7 KB | Display | PDB format |
PDBx/mmJSON format | 1vbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vbb_validation.pdf.gz | 467.5 KB | Display | wwPDB validaton report |
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Full document | 1vbb_full_validation.pdf.gz | 482.2 KB | Display | |
Data in XML | 1vbb_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1vbb_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/1vbb ftp://data.pdbj.org/pub/pdb/validation_reports/vb/1vbb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-POLIOVIRUS TYPE ... , 5 types, 5 molecules 01234
#1: Protein/peptide | Mass: 446.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: P3/SABIN PREPARED FROM A LOW-PASSAGE SEED STOCK OF A PLAQUE ISOLATE (P3/LEON/12A(1)B PLACQUE 411) OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS CONTROL, LONDON) Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B) Genus: Enterovirus / Species: Poliovirus / Strain: P3-SABIN |
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#2: Protein | Mass: 33523.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: P3/SABIN PREPARED FROM A LOW-PASSAGE SEED STOCK OF A PLAQUE ISOLATE (P3/LEON/12A(1)B PLACQUE 411) OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS CONTROL, LONDON) Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B) Genus: Enterovirus / Organ: SEED / Species: Poliovirus / Strain: P3-SABIN / References: UniProt: P03302 |
#3: Protein | Mass: 30169.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: P3/SABIN PREPARED FROM A LOW-PASSAGE SEED STOCK OF A PLAQUE ISOLATE (P3/LEON/12A(1)B PLACQUE 411) OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS CONTROL, LONDON) Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B) Genus: Enterovirus / Organ: SEED / Species: Poliovirus / Strain: P3-SABIN / References: UniProt: P03302 |
#4: Protein | Mass: 25950.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: P3/SABIN PREPARED FROM A LOW-PASSAGE SEED STOCK OF A PLAQUE ISOLATE (P3/LEON/12A(1)B PLACQUE 411) OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS CONTROL, LONDON) Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B) Genus: Enterovirus / Organ: SEED / Species: Poliovirus / Strain: P3-SABIN / References: UniProt: P03302 |
#5: Protein | Mass: 7320.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: P3/SABIN PREPARED FROM A LOW-PASSAGE SEED STOCK OF A PLAQUE ISOLATE (P3/LEON/12A(1)B PLACQUE 411) OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE FOR BIOLOGICAL STANDARDS CONTROL, LONDON) Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B) Genus: Enterovirus / Organ: SEED / Species: Poliovirus / Strain: P3-SABIN / References: UniProt: P03302 |
-Non-polymers , 2 types, 2 molecules
#6: Chemical | ChemComp-J80 / ( |
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#7: Chemical | ChemComp-MYR / |
-Details
Sequence details | THE APPROPRIATE SEQUENCE FOR THIS VIRUS CORRESPONDS TO THE STANWAY ET AL. REFERENCE ABOVE. THE ...THE APPROPRIAT |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 30 % |
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Crystal grow | *PLUS Method: other / Details: Filman, D.J., (1989) EMBO, J., 8, 1567. |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 167372 / % possible obs: 31 % / Observed criterion σ(I): 0 |
Reflection | *PLUS Num. measured all: 395809 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.278 / Highest resolution: 2.8 Å Details: STEREOCHEMICAL CONSTRAINTS BASED ON PARAM19 AND TOP19 FILES USED IN X-PLOR VERSIONS PREVIOUS TO VERSION 3.1 ATOMIC MODELS FOR THE VIRUS AND THE DRUG WERE BUILT TO FIT ICOSAHEDRALLY ...Details: STEREOCHEMICAL CONSTRAINTS BASED ON PARAM19 AND TOP19 FILES USED IN X-PLOR VERSIONS PREVIOUS TO VERSION 3.1 ATOMIC MODELS FOR THE VIRUS AND THE DRUG WERE BUILT TO FIT ICOSAHEDRALLY CONSTRAINED 'FO' MAP USING THE GRAPHICS PROGRAM FRODO (JONES, 1978) MODIFIED TO INCORPORATE T = 1 ICOSAHEDRAL SYMMETRY. ATOMIC MODELS WERE OPTIMIZED WITH RESPECT TO THIS MAP BY A PSEUDO-REAL-SPACE REFINEMENT PROCEDURE, MINIMIZING A RESIDUAL WITH A STEREOCHEMICAL AND A CRYSTALLOGRAPHIC COMPONENT. THE GRADIENT OF THE STEREOCHEMICAL COMPONENT WAS PROVIDED BY THE X-PLOR PROGRAM (A. BRUNGER, X-PLOR VERSION 2.1 YALE UNIVERSITY 1990). THE CRYSTALLOGRAPHIC COMPONENT AND ITS GRADIENT WERE EVALUATED OVER THE VOLUME OF AN ARBITRARY PSEUDO-CELL (THE PROTOMER BOX) WHICH IS SUFFICIENTLY LARGE TO COMFORTABLY ENCLOSE A COMPLETE CHEMICALLY CONTINUOUS POLIOVIRUS PROTOMER, TOGETHER WITH WHATEVER FRAGMENTS OF SYMMETRY-RELATED PROTOMERS HAPPEN TO LIE SUFFICIENTLY CLOSE TO THE BOX TO CONTRIBUTE TO IT. THIS REFINEMENT SEEKS TO MINIMIZE THE DISCREPANCY BETWEEN THE 'PHASED' FOURIER TRANSFORMS OF MODEL-BASED ELECTRON DENSITY AND AUTHENTIC SYMMETRY-CONSTRAINED ELECTRON DENSITY, WHEN EACH TRANSFORM IS CALCULATED IN THE ARBITRARY PROTOMER BOX VOLUME, SCALED IN A RESOLUTION-DEPENDENT FASHION. SEE JRNL REFERENCE FOR MORE DETAILS. THE DISORDERED RESIDUES ABSENT FROM THE MODEL INCLUDE THE AMINO TERMINUS OF VP1 PRIOR TO THE RESIDUE LABELED GLN 24, 1 - 5 IN VP2, 236 - 238 IN VP3, AND THE RESIDUES LABELED 17 - 22 IN VP4. THE POLYPEPTIDE DESIGNATED IN THIS FILE AS RESIDUES 6 - 9 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. NO SOLVENT MOLECULES ARE INCLUDED. THE POLYPEPTIDE DESIGNATED IN THIS FILE AS RESIDUES 6 - 9 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 step | Cycle: LAST / Highest resolution: 2.8 Å
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Refine LS restraints |
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Software | *PLUS Name: 'PSEUDO-REAL SPACE PROCEDURE' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.278 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |