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- PDB-8tuu: MW Polyomavirus LTA bipartite NLS bound to importin alpha 2 -

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Basic information

Entry
Database: PDB / ID: 8tuu
TitleMW Polyomavirus LTA bipartite 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


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 replication origin binding / protein import into nucleus / cytoplasmic stress granule / host cell ...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 replication origin binding / protein import into nucleus / cytoplasmic stress granule / host cell / DNA-binding transcription factor binding / DNA replication / postsynaptic density / hydrolase activity / 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. / Chaperone J-domain superfamily / 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 / Large T-antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MW polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 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)57,9472
Polymers57,9472
Non-polymers00
Water1,892105
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)77.390, 90.067, 100.146
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: 2678.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) MW polyomavirus / References: UniProt: R4L0R1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.7 M sodium citrate, 0.1 M HEPES pH 7.5, 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: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→29.35 Å / Num. obs: 24858 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 43.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.05 / Rrim(I) all: 0.13 / Net I/σ(I): 11.9
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 2 / Num. unique obs: 2728 / CC1/2: 0.7 / Rpim(I) all: 0.45 / Rrim(I) all: 1.18

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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: 2.5→29.35 Å / SU ML: 0.3478 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5857
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 1242 5.01 %
Rwork0.2021 23566 -
obs0.2037 24808 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.57 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 0 105 3457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223433
X-RAY DIFFRACTIONf_angle_d0.51274675
X-RAY DIFFRACTIONf_chiral_restr0.0353559
X-RAY DIFFRACTIONf_plane_restr0.0042599
X-RAY DIFFRACTIONf_dihedral_angle_d15.32391277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.3411450.28532540X-RAY DIFFRACTION99.96
2.6-2.720.34161530.26562563X-RAY DIFFRACTION100
2.72-2.860.29251410.23632582X-RAY DIFFRACTION99.96
2.86-3.040.29931230.23882600X-RAY DIFFRACTION99.96
3.04-3.280.30381350.24012596X-RAY DIFFRACTION99.96
3.28-3.60.24611440.20162613X-RAY DIFFRACTION100
3.6-4.120.19471310.17312620X-RAY DIFFRACTION100
4.12-5.190.17591560.16412648X-RAY DIFFRACTION100
5.19-29.350.19641140.1912804X-RAY DIFFRACTION99.93

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