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- PDB-5mjv: Rebuild and re-refined model for Human Parechovirus 1 -

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Basic information

Entry
Database: PDB / ID: 5mjv
TitleRebuild and re-refined model for Human Parechovirus 1
Components
  • CAPSID SUBUNIT VP0
  • CAPSID SUBUNIT VP1
  • CAPSID SUBUNIT VP3
  • RNA (5'-R(*GP*UP*UP*UP*UP*U)-3')
KeywordsVIRUS / PARECHOVIRUS / PICORNAVIRUS / RNA / HUMAN PARECHOVIRUS 1 / HPeV1 / HPEV
Function / homology
Function and homology information


host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...host cell nucleolus / host cell Golgi membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding / membrane
Similarity search - Function
Viral polyprotein, parechovirus P3B / Parechovirus Genome-linked protein / Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / LRAT domain / LRAT domain profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) ...Viral polyprotein, parechovirus P3B / Parechovirus Genome-linked protein / Viral polyprotein, parechovirus P3A / Picornaviridae P3A protein / LRAT domain / LRAT domain profile. / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Jelly Rolls - #20 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / 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
RNA / Genome polyprotein
Similarity search - Component
Biological speciesHuman parechovirus 1
Echovirus 22
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsShakeel, S. / Dykeman, E.C. / White, S.J. / Ora, A. / Cockburn, J.J.B. / Butcher, S.J. / Stockley, P.G. / Twarock, R.
Funding support Finland, United Kingdom, 8items
OrganizationGrant numberCountry
Academy of Finland139178 Finland
Academy of Finand275199 Finland
Sigrid Juselius Foundation Finland
Wellcome Trust062164 United Kingdom
Wellcome Trust090932/Z/09/Z United Kingdom
Wellcome Trust097827/Z/11/Z United Kingdom
Leverhulme TrustLT130088 United Kingdom
Leverhulme Trust Research FellowshipECF2013-019 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Genomic RNA folding mediates assembly of human parechovirus.
Authors: Shakeel, S. / Dykeman, E.C. / White, S.J. / Ora, A. / Cockburn, J.J. / Butcher, S.J. / Stockley, P.G. / Twarock, R.
History
DepositionDec 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
SupersessionMar 8, 2017ID: 5M74
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAPSID SUBUNIT VP1
B: CAPSID SUBUNIT VP3
C: CAPSID SUBUNIT VP0
D: RNA (5'-R(*GP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)88,2354
Polymers88,2354
Non-polymers00
Water00
1
A: CAPSID SUBUNIT VP1
B: CAPSID SUBUNIT VP3
C: CAPSID SUBUNIT VP0
D: RNA (5'-R(*GP*UP*UP*UP*UP*U)-3')
x 60


Theoretical massNumber of molelcules
Total (without water)5,294,110240
Polymers5,294,110240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area11770 Å2
ΔGint-64 kcal/mol
Surface area34730 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: CAPSID SUBUNIT VP1
B: CAPSID SUBUNIT VP3
C: CAPSID SUBUNIT VP0
D: RNA (5'-R(*GP*UP*UP*UP*UP*U)-3')
x 5


  • icosahedral pentamer
  • 441 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)441,17620
Polymers441,17620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: CAPSID SUBUNIT VP1
B: CAPSID SUBUNIT VP3
C: CAPSID SUBUNIT VP0
D: RNA (5'-R(*GP*UP*UP*UP*UP*U)-3')
x 6


  • icosahedral 23 hexamer
  • 529 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)529,41124
Polymers529,41124
Non-polymers00
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
Unit cell
Length a, b, c (Å)399.500, 399.500, 332.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein CAPSID SUBUNIT VP1


Mass: 26417.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parechovirus 1 (strain Harris) / Strain: Harris / Cell line (production host): A549 / Organ (production host): LUNG / Production host: Homo sapiens (human) / Tissue (production host): LUNG CARCINOMA
References: UniProt: Q66578, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein CAPSID SUBUNIT VP3


Mass: 28293.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parechovirus 1 (strain Harris) / Strain: Harris / Cell line: A549 / Cell line (production host): A549 / Organ (production host): LUNG / Production host: Homo sapiens (human) / Tissue (production host): LUNG CARCINOMA
References: UniProt: Q66578, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein CAPSID SUBUNIT VP0


Mass: 31693.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parechovirus 1 (strain Harris) / Strain: Harris / Cell line (production host): A549 / Organ (production host): LUNG / Production host: Homo sapiens (human) / Tissue (production host): LUNG CARCINOMA
References: UniProt: Q66578, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: RNA chain RNA (5'-R(*GP*UP*UP*UP*UP*U)-3')


Mass: 1831.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echovirus 22 (strain Harris) / Cell line (production host): A549 / Organ (production host): LUNG / Production host: Homo sapiens (human) / Tissue (production host): LUNG CARCINOMA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M TRIS PH 8.0, 0.6M AMMONIUM SULFATE, 0.1M MGCL2, 5% (W/V) GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.09→345.977 Å / Num. obs: 233083 / % possible obs: 78.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.354 / Net I/σ(I): 5
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 0.9 / % possible all: 31.8

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
CNS1.3refinement
REFMAC5.8.0135refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BEV

1bev


Resolution: 3.09→345.977 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2612 -5 %
Rwork0.2584 --
obs0.2584 221407 82.7405 %
Refinement stepCycle: LAST / Resolution: 3.09→345.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5285 119 0 0 5404

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