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- PDB-8tuq: STL Polyomavirus LTA NLS bound to importin alpha 2 -

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Basic information

Entry
Database: PDB / ID: 8tuq
TitleSTL Polyomavirus LTA NLS bound to importin alpha 2
Components
  • Importin subunit alpha-1
  • Large T antigen
KeywordsTRANSPORT PROTEIN / importin / karyopherin / nuclear / nls
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / 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 / nuclear import signal receptor activity / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / 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 / nuclear import signal receptor activity / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / DNA replication / hydrolase activity / postsynaptic density / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / glutamatergic synapse / nucleoplasm / ATP binding / metal ion binding / cytosol
Similarity search - Function
Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / Importin subunit alpha ...Large T antigen, polyomaviridae / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / 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. / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / 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
Large T antigen / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
STL polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDonnelly, C.M. / Cross, E.M. / Forwood, J.K. / Alvisi, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: A functional and structural comparative analysis of large tumor antigens reveals evolution of different importin alpha-dependent nuclear localization signals.
Authors: Cross, E.M. / Akbari, N. / Ghassabian, H. / Hoad, M. / Pavan, S. / Ariawan, D. / Donnelly, C.M. / Lavezzo, E. / Petersen, G.F. / Forwood, J.K. / Alvisi, G.
History
DepositionAug 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year

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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: Large T antigen


Theoretical massNumber of molelcules
Total (without water)57,6312
Polymers57,6312
Non-polymers00
Water4,594255
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)78.268, 89.803, 100.655
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 Large T antigen


Mass: 2362.682 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) STL polyomavirus / References: UniProt: L7REU2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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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: 59.92 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.80 M sodium citrate, 0.1 M HEPES pH 6.5, 0.01 M 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: Sep 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2→29.21 Å / Num. obs: 47684 / % possible obs: 98.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 31.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.03 / Rrim(I) all: 0.06 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3523 / CC1/2: 0.84 / Rpim(I) all: 0.31 / Rrim(I) all: 0.67

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.20.1_4487refinement
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.21 Å / SU ML: 0.1987 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1996 2453 5.15 %
Rwork0.1659 45177 -
obs0.1676 47630 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.02 Å2
Refinement stepCycle: LAST / Resolution: 2→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3409 0 0 255 3664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01043503
X-RAY DIFFRACTIONf_angle_d0.99984775
X-RAY DIFFRACTIONf_chiral_restr0.0558571
X-RAY DIFFRACTIONf_plane_restr0.0089615
X-RAY DIFFRACTIONf_dihedral_angle_d13.51291296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.29031430.24412472X-RAY DIFFRACTION99.28
2.04-2.080.25991330.21722527X-RAY DIFFRACTION99.36
2.08-2.130.23341410.20092497X-RAY DIFFRACTION99.17
2.13-2.170.24421330.19442504X-RAY DIFFRACTION98.99
2.17-2.230.22381400.18522502X-RAY DIFFRACTION99.06
2.23-2.290.21431530.18072496X-RAY DIFFRACTION98.92
2.29-2.360.2061430.16492471X-RAY DIFFRACTION98.68
2.36-2.430.21461310.16862512X-RAY DIFFRACTION98.62
2.43-2.520.20411520.16722499X-RAY DIFFRACTION98.7
2.52-2.620.22481380.16542497X-RAY DIFFRACTION98.47
2.62-2.740.23931340.17492495X-RAY DIFFRACTION97.99
2.74-2.880.19561300.17532514X-RAY DIFFRACTION97.82
2.88-3.060.21471240.17982519X-RAY DIFFRACTION97.74
3.06-3.30.18661190.1762501X-RAY DIFFRACTION97.14
3.3-3.630.19811340.16492516X-RAY DIFFRACTION97.32
3.63-4.160.18981120.14022538X-RAY DIFFRACTION97
4.16-5.230.16821430.13642529X-RAY DIFFRACTION96.15
5.23-29.210.17811500.16492588X-RAY DIFFRACTION94.71

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