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Yorodumi- PDB-1pvc: REFINEMENT OF THE SABIN STRAIN OF TYPE 3 POLIOVIRUS AT 2.4 ANGSTR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pvc | ||||||
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Title | REFINEMENT OF THE SABIN STRAIN OF TYPE 3 POLIOVIRUS AT 2.4 ANGSTROMS AND THE CRYSTAL STRUCTURES OF ITS VARIANTS AT 2.9 ANGSTROMS RESOLUTION | ||||||
Components | (POLIOVIRUS TYPE 3, SABIN ...) x 5 | ||||||
Keywords | VIRUS / 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: 2.4 Å | ||||||
Authors | Syed, R. / Filman, D.J. / Hogle, J.M. | ||||||
Citation | Journal: To be Published Title: Refinement of the Sabin Strain of Type 3 Poliovirus at 2.4 Angstroms and the Crystal Structures of its Variants at 2.9 Angstroms Resolution Authors: Syed, R. / Filman, D.J. / Hogle, J.M. #1: Journal: Use of X-Ray Crystallography in the Design of Antiviral Agents Year: 1990 Title: Structural Determinants of Serotype Specificity Host Range and Thermostability in Poliovirus Authors: Hogle, J.M. / Syed, R. / Yeates, T.O. / Jacobson, D. / Filman, D.J. #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: Vaccines 89: Modern Approaches to New Vaccines Including Prevention of Aids Year: 1989 Title: Structural Determinants of Serotype Specificity in Poliovirus Authors: Hogle, J.M. / Filman, D.J. / Critchlow, T. / Jacobson, D. / Yeates, T.O. / Syed, R. #5: Journal: Concepts in Viral Pathogenesis III / Year: 1989 Title: Structural Determinants of Serotype Specificity and Host Range in Poliovirus Authors: Hogle, J.M. / Syed, R. / Yeates, T.O. / Jacobson, D. / Critchlow, T. / Filman, D.J. #6: Journal: Molecular Aspects of Picornavirus Infection and Detection Year: 1989 Title: Structural Basis for Serotypic Differences and Thermostability in Poliovirus Authors: Hogle, J.M. / Filman, D.J. / Syed, R. / Chow, M. / Minor, P.D. #7: Journal: Nucleic Acids Res. / Year: 1983 Title: The Nucleotide Sequence of Poliovirus Type 3 Leon 12A(1)B: 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 |
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Remark 700 | SHEET STRANDS 2, 3, AND 4 ARE COMMON TO SHEETS *1B1* AND *1B2*. THE SECOND STRAND OF SHEET *1B3* IS ...SHEET STRANDS 2, 3, AND 4 ARE COMMON TO SHEETS *1B1* AND *1B2*. THE SECOND STRAND OF SHEET *1B3* IS THE SAME AS THE THIRD STRAND OF SHEETS *1B1* AND *1B2*. STRANDS 1, 2, AND 3 ARE COMMON TO SHEETS *2B1*, *2B2*, AND *2B3*. STRANDS 1 AND 2 ARE COMMON TO SHEETS *2C1*, *2C2*, AND *2C3*. THE LAST FOUR STRANDS ARE COMMON TO SHEETS *3B1* AND *3B2*. SEQUENCE NUMBERING IS UNCERTAIN IN THE THIRD STRAND OF SHEET * 4N*. SHEET * 3C* CONSISTS OF SEVEN STRANDS. THE FIFTH AND SIXTH STRANDS OF SHEET * 3C* ARE FROM A THREEFOLD-RELATED PROTOMER. BECAUSE OF LIMITATIONS IMPOSED BY THE PROTEIN DATA BANK FORMAT IT IS NOT POSSIBLE TO PRESENT ALL OF THIS SHEET ON SHEET RECORDS. INSTEAD THE COMPLETE SHEET IS SPECIFIED IN THIS REMARK. 3C 7 LEU 3 83 LEU 3 87 0 3C 7 GLY 3 188 PHE 3 193 -1 O GLY 3 188 N LEU 3 87 3C 7 ALA 3 126 ALA 3 135 -1 O ALA 3 135 N TYR 3 189 3C 7 THR 3 152 TRP 3 156 -1 O THR 3 152 N TYR 3 134 3C 7 ASN 2 20 THR 2 25 1 O ASN 2 20 N HIS 3 153 3C 7 LEU 2 14 LEU 2 18 -1 O LEU 2 18 N SER 2 21 3C 7 ALA 1 36 SER 1 38 -1 N ALA 1 36 O THR 2 17 SHEET * TT* CONSISTS OF FIVE STRANDS. ALL FIVE STRANDS OF SHEET * TT* ARE FROM FIVE-FOLD-RELATED PROTOMERS. BECAUSE OF LIMITATIONS IMPOSED BY THE PROTEIN DATA BANK FORMAT IT IS NOT POSSIBLE TO PRESENT THIS SHEET ON SHEET RECORDS. INSTEAD THIS SHEET IS SPECIFIED IN THIS REMARK. TT 5 LEU 3 2 THR 3 7 0 TT 5 LEU 3 2 THR 3 7 1 N LEU 3 2 O PRO 3 3 TT 5 LEU 3 2 THR 3 7 1 N LEU 3 2 O PRO 3 3 TT 5 LEU 3 2 THR 3 7 1 N LEU 3 2 O PRO 3 3 TT 5 LEU 3 2 THR 3 7 1 N LEU 3 2 O PRO 3 3 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pvc.cif.gz | 192.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pvc.ent.gz | 148.5 KB | Display | PDB format |
PDBx/mmJSON format | 1pvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pvc_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
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Full document | 1pvc_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | 1pvc_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 1pvc_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/1pvc ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pvc | HTTPS FTP |
-Related structure data
Similar structure data |
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-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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Atom site foot note | 1: CIS PROLINE - PRO 2 83 | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-POLIOVIRUS TYPE 3, SABIN ... , 5 types, 5 molecules 01234
#1: Protein/peptide | Mass: 446.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: SEED STOCK OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE OF BIOLOGICAL STANDARDS AND CONTROL, LONDON) Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B) Genus: Enterovirus / Species: Poliovirus Strain: DERIVED FROM LABORATORY STRAIN P3/LEON/12A(1)B PLACQUE 411 |
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#2: Protein | Mass: 33651.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: SEED STOCK OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE OF BIOLOGICAL STANDARDS AND CONTROL, LONDON) Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B) Genus: Enterovirus / Species: Poliovirus Strain: DERIVED FROM LABORATORY STRAIN P3/LEON/12A(1)B PLACQUE 411 References: PIR: S03822, UniProt: P03302*PLUS |
#3: Protein | Mass: 30169.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: SEED STOCK OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE OF BIOLOGICAL STANDARDS AND CONTROL, LONDON) Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B) Genus: Enterovirus / Species: Poliovirus Strain: DERIVED FROM LABORATORY STRAIN P3/LEON/12A(1)B PLACQUE 411 References: UniProt: P03302 |
#4: Protein | Mass: 26289.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: SEED STOCK OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE OF BIOLOGICAL STANDARDS AND CONTROL, LONDON) Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B) Genus: Enterovirus / Species: Poliovirus Strain: DERIVED FROM LABORATORY STRAIN P3/LEON/12A(1)B PLACQUE 411 References: PIR: S03822, UniProt: P03302*PLUS |
#5: Protein | Mass: 7320.917 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: SEED STOCK OBTAINED FROM P.D.MINOR (NATIONAL INSTITUTE OF BIOLOGICAL STANDARDS AND CONTROL, LONDON) Source: (natural) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B) Genus: Enterovirus / Species: Poliovirus Strain: DERIVED FROM LABORATORY STRAIN P3/LEON/12A(1)B PLACQUE 411 References: UniProt: P03302 |
-Non-polymers , 3 types, 425 molecules
#6: Chemical | ChemComp-SPH / |
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#7: Chemical | ChemComp-MYR / |
#8: Water | ChemComp-HOH / |
-Details
Compound details | THE MYRISTOYL MOIETY, MYR, IS COVALENTLYNonpolymer details | ALTHOUGH ALL OF THE SOLVENT MOLECULES IN THIS FILE HAVE BEEN DESIGNATED TO BE WATER MOLECULES, ...ALTHOUGH ALL OF THE SOLVENT MOLECULES IN THIS FILE HAVE BEEN DESIGNATED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Data collection
Reflection | Resolution: 2.4→30 Å / Num. obs: 520979 / % possible obs: 61.6 % |
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-Processing
Software |
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Refinement | Resolution: 2.4→10 Å / σ(F): 0 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. SOLVENT MOLECULES HAVE BEEN ASSIGNED INDIVIDUAL OCCUPANCY VALUES BY THE PSEUDO-REAL-SPACE REFINEMENT PROCEDURE AND AN OVERALL TEMPERATURE FACTOR BY THE XPLOR PROGRAM. RESIDUE 1000 IS IDENTIFIED AS A SPHINGOSINE MOLECULE (SPH). THE PROVISIONAL IDENTIFICATION OF ELECTRON DENSITY AS SPHINGOSINE IS NOT BASED ON DIRECT CHEMICAL EVIDENCE.
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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