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- PDB-4z92: crystal structure of parechovirus-1 virion -

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Basic information

Entry
Database: PDB / ID: 4z92
Titlecrystal structure of parechovirus-1 virion
Components
  • Capsid subunit VP3
  • RNA (5'-R(*AP*UP*UP*UP*UP*U)-3')
  • capsid subunit VP0
  • capsid subunit VP1
KeywordsVIRUS / parechovirus / picornavirus / virion / pathogen
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKalynych, S. / Palkova, L. / Plevka, P.
CitationJournal: J.Virol. / Year: 2015
Title: The Structure of Human Parechovirus 1 Reveals an Association of the RNA Genome with the Capsid.
Authors: Kalynych, S. / Palkova, L. / Plevka, P.
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: cell / chem_comp_atom ...cell / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_oper
Item: _cell.Z_PDB / _database_2.pdbx_DOI ..._cell.Z_PDB / _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(*AP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)88,2194
Polymers88,2194
Non-polymers00
Water00
1
A: capsid subunit VP1
B: Capsid subunit VP3
C: capsid subunit VP0
D: RNA (5'-R(*AP*UP*UP*UP*UP*U)-3')
x 60


Theoretical massNumber of molelcules
Total (without water)5,293,150240
Polymers5,293,150240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area11610 Å2
ΔGint-61 kcal/mol
Surface area34830 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(*AP*UP*UP*UP*UP*U)-3')
x 5


  • icosahedral pentamer
  • 441 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)441,09620
Polymers441,09620
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(*AP*UP*UP*UP*UP*U)-3')
x 6


  • icosahedral 23 hexamer
  • 529 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)529,31524
Polymers529,31524
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
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.642324, -0.755791, 0.127343), (-0.178391, -0.309024, -0.934235), (0.745348, 0.57738, -0.3333)148.0114, 264.3406, -104.5197
3generate(-0.142303, -0.467073, 0.872691), (0.467127, -0.808997, -0.356855), (0.872656, 0.356885, 0.3333)209.4198, 145.0114, -159.9919
4generate(0.475675, 0.46709, -0.745391), (0.11029, 0.809025, 0.577345), (0.872691, -0.356855, 0.3333)112.894, -48.0498, -77.6859
5generate(0.745367, 1.0E-5, 0.666693), (1.0E-5, -1.000067, -5.4E-5), (0.666693, -5.4E-5, -0.7453)-4.6171, 230.6623, 12.0694
6generate(0.475653, -0.467073, -0.745348), (-0.110273, 0.809047, -0.57738), (0.872657, 0.356885, 0.3333)220.628, 92.0956, -159.9919
7generate(0.642344, 0.755773, 0.127352), (0.178373, -0.309044, 0.93418), (0.745391, -0.577345, -0.3333)-26.3162, 37.599, 28.6416
8generate(0.563654, 0.755753, 0.33335), (-0.755747, 0.309046, 0.577379), (0.333306, -0.577296, 0.7454)-27.7376, 182.5989, 21.1858
9generate(-0.142303, 0.467127, 0.872657), (-0.467073, -0.808997, 0.356885), (0.872691, -0.356855, 0.3333)101.6851, 272.224, -77.6859
10generate(0.563654, -0.755748, 0.333306), (0.755753, 0.309046, -0.577296), (0.33335, 0.577379, 0.7454)46.5813, -23.2369, -111.987

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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) / Cell line (production host): A549 / Organ (production host): Lung / Production host: Homo sapiens (human) / Tissue (production host): lung carcinoma / References: UniProt: Q66578
#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) / 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
#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) / Cell line (production host): A549 / Organ (production host): Lung / Production host: Homo sapiens (human) / Tissue (production host): lung carcinoma / References: UniProt: Q66578
#4: RNA chain RNA (5'-R(*AP*UP*UP*UP*UP*U)-3')


Mass: 1815.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human parechovirus 1 (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

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris pH 8.0, 0.6M ammonium sulfate, 0.1M MgCl2, 5% (w/v) glycerol

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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→65 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
CNS1.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BEV

1bev


Resolution: 3.1→65 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rwork0.29 --
obs-233083 78.2 %
Refinement stepCycle: LAST / Resolution: 3.1→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5285 119 0 0 5404

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