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- PDB-1pov: ROLE AND MECHANISM OF THE MATURATION CLEAVAGE OF VP0 IN POLIOVIRU... -

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Entry
Database: PDB / ID: 1pov
TitleROLE AND MECHANISM OF THE MATURATION CLEAVAGE OF VP0 IN POLIOVIRUS ASSEMBLY: STRUCTURE OF THE EMPTY CAPSID ASSEMBLY INTERMEDIATE AT 2.9 ANGSTROMS RESOLUTION
Components(POLIOVIRUS NATIVE EMPTY CAPSID (TYPE ...) x 3
KeywordsVIRUS / PICORNAVIRUS / Icosahedral virus / Virus
Function / homologyPoliovirus 3A protein-like / Viral coat protein subunit / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / picornavirus capsid protein ...Poliovirus 3A protein-like / Viral coat protein subunit / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / picornavirus capsid protein / Picornavirus 2B protein / 3C cysteine protease (picornain 3C) / Picornavirus coat protein VP4 / RNA-directed RNA polymerase, catalytic domain / RNA dependent RNA polymerase / RNA helicase / Picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus coat protein (VP4) / Poliovirus 3A protein like / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded RNA virus / Peptidase C3, picornavirus core protein 2A / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / T=pseudo3 icosahedral viral capsid / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / virion assembly / viral capsid / RNA-directed RNA polymerase / induction by virus of host autophagy / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein
Function and homology information
Specimen sourceHuman poliovirus 1
MethodX-RAY DIFFRACTION / 2.8 Å resolution
AuthorsBasavappa, R. / Filman, D.J. / Hogle, J.M.
Citation
Journal: Protein Sci. / Year: 1994
Title: Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: structure of the empty capsid assembly intermediate at 2.9 A resolution.
Authors: Basavappa, R. / Syed, R. / Flore, O. / Icenogle, J.P. / Filman, D.J. / Hogle, J.M.
#1: Journal: Embo J. / Year: 1991
Title: Three-Dimensional Structure of a Mouse-Adapted Type 2(Slash)Type 1 Poliovirus Chimera
Authors: Yeates, T.O. / Jacobson, D.H. / Martin, A. / Wychowski, C. / Girard, M. / Filman, D.J. / Hogle, J.M.
#2: 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.
#3: Journal: Nature / Year: 1987
Title: Myristylation of Picornavirus Capsid Protein Vp4 and its Structural Significance
Authors: Chow, M. / Newman, J.F.E. / Filman, D. / Hogle, J.M. / Rowlands, D.J. / Brown, F.
#4: Journal: Science / Year: 1985
Title: Three-Dimensional Structure of Poliovirus at 2.9 Angstroms Resolution
Authors: Hogle, J.M. / Chow, M. / Filman, D.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 10, 1995 / Release: Dec 7, 1995
RevisionDateData content typeGroupProviderType
1.0Dec 7, 1995Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelSource and taxonomy / Version format compliance
Remark 285THE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE CRYSTAL ASYMMETRIC UNIT. IN ADDITION, THE ...THE ENTRY PRESENTED HERE DOES NOT CONTAIN THE COMPLETE CRYSTAL ASYMMETRIC UNIT. IN ADDITION, THE COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. IN ORDER TO GENERATE THE FULL CRYSTAL AU, APPLY THE FOLLOWING TRANSFORMATION MATRIX OR MATRICES AND SELECTED BIOMT RECORDS TO THE COORDINATES, AS SHOWN BELOW. X0 1 0.999288 -0.037725 0.000000 0.00000 X0 2 0.037725 0.999288 0.000000 0.00000 X0 3 0.000000 0.000000 1.000000 -94.92208 CRYSTAL AU = (X0) * (BIOMT 1-5,11-15,21-30,41-50) * CHAINS 0,1,3
Remark 700SHEET THE SHEET RECORDS DO NOT LIST BETA INTERACTIONS BETWEEN SYMMETRY-RELATED PROTOMERS. THESE ...SHEET THE SHEET RECORDS DO NOT LIST BETA INTERACTIONS BETWEEN SYMMETRY-RELATED PROTOMERS. THESE INCLUDE FIVE-STRANDED BETA TUBES AROUND THE FIVE-FOLD AXES, AS WELL AS EXTENDED SIX-STRANDED SHEETS WHICH JOIN SHEET K FROM ONE PROTOMER WITH SHEET B FROM ANOTHER PROTOMER. HYDROGEN BONDING PATTERNS IN THE BETA TUBES ARE IDENTICAL TO THOSE DESCRIBED IN THE REMARKS OF ENTRY 2PLV.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
1: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
3: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0155
Polyers97,4873
Non-polymers5282
Water3,783210
1
0: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
1: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
3: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,880,883300
Polyers5,849,211180
Non-polymers31,672120
Water3,243180
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
0: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
1: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
3: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
hetero molecules
x 5


  • icosahedral pentamer
  • 490 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)490,07425
Polyers487,43415
Non-polymers2,63910
Water27015
TypeNameSymmetry operationNumber
point symmetry operation5
4
0: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
1: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
3: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 588 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)588,08830
Polyers584,92118
Non-polymers3,16712
Water32418
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 NATIVE EMPTY CAPSID (TYPE 1)
1: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
3: POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.94 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)2,940,441150
Polyers2,924,60690
Non-polymers15,83660
Water1,62190
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation30
Unit cell
γ
α
β
Length a, b, c (Å)322.900, 358.000, 380.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2
Atom site foot note1: CIS PROLINE - PRO 0 152

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Components

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POLIOVIRUS NATIVE EMPTY CAPSID (TYPE ... , 3 types, 3 molecules 013

#1: Protein/peptide POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)


Mass: 37450.758 Da / Num. of mol.: 1 / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#2: Protein/peptide POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)


Mass: 33488.613 Da / Num. of mol.: 1 / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#3: Protein/peptide POLIOVIRUS NATIVE EMPTY CAPSID (TYPE 1)


Mass: 26547.482 Da / Num. of mol.: 1 / Source: (natural) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300

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Non-polymers , 3 types, 212 molecules

#4: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Formula: C14H28O2 / Myristic acid
#5: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Formula: C18H37NO2 / Sphingosine
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Formula: H2O / Water

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Details

Compound detailsPOLIOVIRUS EMPTY CAPSID PRODUCED BY INFECTING HELA CELLS WITH P1/MAHONEY POLIOVIRUS AND INHIBITING ...POLIOVIRUS EMPTY CAPSID PRODUCED BY INFECTING HELA CELLS WITH P1/MAHONEY POLIOVIRUS AND INHIBITING POLIOVIRUS RNA SYNTHESIS PART WAY IN THE INFECTION CYCLE (SEE BASAVAPPA ET AL. FOR DETAILS).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Temp: 4 ℃ / pH: 7 / Method: microdialysis
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
115 mg/mlcapsid11
20.8 M11NaCl
310 mMPIPES11
45 mM11MgCl2
51 mM11CaCl2
60.05 M12NaCl
710 mMPIPES12
85 mM12MgCl2
91 mM12CaCl2

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Data collection

ReflectionNumber obs: 610509 / Percent possible obs: 61.7
Reflection
*PLUS
Number measured all: 1885617 / Rmerge I obs: 0.189

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
Displacement parametersB iso mean: 18.86
Least-squares processR factor obs: 0.281 / Highest resolution: 2.8 / Lowest resolution: 3 / Number reflection obs: 607564
Refine hist #LASTHighest resolution: 2.8 / Lowest resolution: 3
Number of atoms included #LASTProtein: 6035 / Nucleic acid: 0 / Ligand: 36 / Solvent: 210 / Total: 6281
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.015
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_deg2.7
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_it1.51.5
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it2.02.0
X-RAY DIFFRACTIONo_scangle_it

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