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- PDB-8f2q: Human Parvovirus B19 Nonstructural NS1 Protein NLS bound to Impor... -

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Basic information

Entry
Database: PDB / ID: 8f2q
TitleHuman Parvovirus B19 Nonstructural NS1 Protein NLS bound to Importin Alpha 2
Components
  • Importin subunit alpha-1
  • Initiator protein NS1
KeywordsTRANSPORT PROTEIN / Importin / nuclear / transport / nls
Function / homology
Function and homology information


rolling hairpin viral DNA replication / symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated perturbation of host transcription / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nuclear import signal receptor activity ...rolling hairpin viral DNA replication / symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont-mediated perturbation of host transcription / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nuclear import signal receptor activity / helicase activity / symbiont-mediated activation of host apoptosis / protein import into nucleus / cytoplasmic stress granule / host cell / DNA helicase / endonuclease activity / DNA-binding transcription factor binding / DNA replication / postsynaptic density / host cell nucleus / glutamatergic synapse / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / cytosol
Similarity search - Function
Rep protein catalytic-like / Rep protein catalytic domain like / : / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / Importin subunit alpha / Atypical Arm repeat ...Rep protein catalytic-like / Rep protein catalytic domain like / : / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Importin subunit alpha-1 / Initiator protein NS1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human parvovirus B19
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCross, E.M. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Antiviral Res. / Year: 2023
Title: Importin alpha / beta-dependent nuclear transport of human parvovirus B19 nonstructural protein 1 is essential for viral replication.
Authors: Alvisi, G. / Manaresi, E. / Cross, E.M. / Hoad, M. / Akbari, N. / Pavan, S. / Ariawan, D. / Bua, G. / Petersen, G.F. / Forwood, J. / Gallinella, G.
History
DepositionNov 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-1
B: Initiator protein NS1
C: Initiator protein NS1


Theoretical massNumber of molelcules
Total (without water)57,6393
Polymers57,6393
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.197, 90.188, 100.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Importin subunit alpha-1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 55268.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide Initiator protein NS1 / NS1 / NCVP1 / Non-capsid protein NS-1 / Non-structural protein 1 / Non-structural protein NS1


Mass: 1185.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human parvovirus B19
References: UniProt: Q9PZT1, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters, DNA helicase

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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

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.7M sodium citrate, 0.1M HEPES pH6.5, 0.01M DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.7→29.54 Å / Num. obs: 20091 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 45.78 Å2 / CC1/2: 0.947 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.3
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 1.045 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2620 / CC1/2: 0.563

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Processing

Software
NameVersionClassification
Aimlessdata scaling
Cootmodel building
PHENIX1.20.1-4487refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4uaf

4uaf


Resolution: 2.7→29.54 Å / SU ML: 0.3467 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1262
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2287 527 2.63 %
Rwork0.215 19507 -
obs0.2154 20034 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.62 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 0 0 3354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313414
X-RAY DIFFRACTIONf_angle_d0.5764645
X-RAY DIFFRACTIONf_chiral_restr0.0361558
X-RAY DIFFRACTIONf_plane_restr0.0046593
X-RAY DIFFRACTIONf_dihedral_angle_d4.1637455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.970.31191320.31314780X-RAY DIFFRACTION99.94
2.97-3.40.31071320.26954826X-RAY DIFFRACTION99.78
3.4-4.280.2411300.20644847X-RAY DIFFRACTION99.6
4.28-29.540.15711330.16925054X-RAY DIFFRACTION99.58

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