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- PDB-8q8k: KI Polyomavirus LTA NLS bound to importin alpha 2 -

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Basic information

Entry
Database: PDB / ID: 8q8k
TitleKI Polyomavirus LTA NLS bound to importin alpha 2
Components
  • Importin subunit alpha-1
  • Large T antigenLarge tumor antigen
KeywordsPROTEIN TRANSPORT / 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 / host cell / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus ...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 / host cell / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / nuclear membrane / DNA-binding transcription factor binding / DNA replication / postsynaptic density / hydrolase activity / glutamatergic synapse / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / nucleoplasm / ATP binding / metal ion binding / nucleus / 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 / Helicase, superfamily 3, DNA virus ...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 / 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. / DnaJ molecular chaperone homology domain / 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)
KI polyomavirus Stockholm 60
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCross, 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 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin subunit alpha-1
B: Importin subunit alpha-1
C: Large T antigen
D: Large T antigen


Theoretical massNumber of molelcules
Total (without water)115,3624
Polymers115,3624
Non-polymers00
Water0
1
A: Importin subunit alpha-1
C: Large T antigen


Theoretical massNumber of molelcules
Total (without water)57,6812
Polymers57,6812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Importin subunit alpha-1
D: Large T antigen


Theoretical massNumber of molelcules
Total (without water)57,6812
Polymers57,6812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.237, 85.696, 139.064
Angle α, β, γ (deg.)90.000, 95.960, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-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.: 2
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 / Large tumor antigen


Mass: 2412.718 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) KI polyomavirus Stockholm 60 / References: UniProt: P0DOI6

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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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.2 M NaCl, 0.1 M Tris pH 8.0, 16 % PEG4000. Protein stock pre-treated with 5:1 molar ratio IMPa: ivermectin

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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: Mar 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.7→19.88 Å / Num. obs: 34296 / % possible obs: 99.2 % / Redundancy: 2.4 % / Biso Wilson estimate: 67.92 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.04 / Rrim(I) all: 0.07 / Net I/σ(I): 8.9
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4564 / CC1/2: 0.76 / Rpim(I) all: 0.43 / Rrim(I) all: 0.67 / % possible all: 99.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→19.88 Å / SU ML: 0.2802 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8368
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2466 1703 4.97 %
Rwork0.2125 32563 -
obs0.2143 34266 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.11 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 0 0 0 6354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266465
X-RAY DIFFRACTIONf_angle_d0.52418835
X-RAY DIFFRACTIONf_chiral_restr0.03581088
X-RAY DIFFRACTIONf_plane_restr0.00391134
X-RAY DIFFRACTIONf_dihedral_angle_d13.65742278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.780.36481300.31832714X-RAY DIFFRACTION99.03
2.78-2.870.3541420.31222676X-RAY DIFFRACTION98.88
2.87-2.970.32941200.30232725X-RAY DIFFRACTION99.09
2.97-3.090.32821510.2912662X-RAY DIFFRACTION98.84
3.09-3.230.33441520.26152699X-RAY DIFFRACTION99.3
3.23-3.40.29661370.26482715X-RAY DIFFRACTION99.69
3.4-3.610.2781470.23732726X-RAY DIFFRACTION99.69
3.61-3.890.24941600.20372704X-RAY DIFFRACTION99.69
3.89-4.280.1931330.17942736X-RAY DIFFRACTION99.62
4.28-4.890.22021370.18162716X-RAY DIFFRACTION99.58
4.89-6.130.23691310.21922747X-RAY DIFFRACTION99.21
6.13-19.880.20291630.16722743X-RAY DIFFRACTION98.18

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