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- PDB-8tur: Merkel Cell Polyomavirus LTA bipartite NLS bound to importin alpha 2 -

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Basic information

Entry
Database: PDB / ID: 8tur
TitleMerkel Cell Polyomavirus LTA bipartite NLS bound to importin alpha 2
Components
  • Importin subunit alpha-1
  • Truncated 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 / protein import into nucleus / cytoplasmic stress granule / host cell / DNA-binding transcription factor binding ...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 / protein import into nucleus / cytoplasmic stress granule / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / cytosol
Similarity search - Function
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. / Chaperone J-domain superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat ...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. / 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
Similarity search - Domain/homology
Truncated large T antigen / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Merkel cell polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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: Truncated large T antigen


Theoretical massNumber of molelcules
Total (without water)59,0352
Polymers59,0352
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.035, 89.498, 99.767
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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 Truncated large T antigen


Mass: 3766.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Merkel cell polyomavirus / References: UniProt: M4VRX3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.65 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: Jun 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.15→24.94 Å / Num. obs: 39199 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 36.77 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.04 / Rrim(I) all: 0.13 / Net I/σ(I): 12.8
Reflection shellResolution: 2.15→2.22 Å / Rmerge(I) obs: 1.29 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3357 / CC1/2: 0.69 / Rpim(I) all: 0.38 / Rrim(I) all: 1.34

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→24.94 Å / SU ML: 0.2179 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1425
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.208 2002 5.12 %
Rwork0.1809 37130 -
obs0.1823 39132 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.5 Å2
Refinement stepCycle: LAST / Resolution: 2.15→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 0 186 3576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273462
X-RAY DIFFRACTIONf_angle_d0.53194710
X-RAY DIFFRACTIONf_chiral_restr0.0361563
X-RAY DIFFRACTIONf_plane_restr0.0036604
X-RAY DIFFRACTIONf_dihedral_angle_d4.1235464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.3081470.26632616X-RAY DIFFRACTION99.96
2.2-2.260.26061480.24082588X-RAY DIFFRACTION99.96
2.26-2.330.24621510.21482621X-RAY DIFFRACTION100
2.33-2.40.25771320.20672613X-RAY DIFFRACTION99.96
2.41-2.490.23241200.19932650X-RAY DIFFRACTION100
2.49-2.590.23451450.20772620X-RAY DIFFRACTION100
2.59-2.710.22611700.20242618X-RAY DIFFRACTION100
2.71-2.850.21411360.18422621X-RAY DIFFRACTION99.93
2.85-3.030.25061290.19752663X-RAY DIFFRACTION99.96
3.03-3.260.23881460.20092637X-RAY DIFFRACTION99.96
3.26-3.590.20451420.18022672X-RAY DIFFRACTION99.93
3.59-4.110.18181400.1562676X-RAY DIFFRACTION100
4.11-5.170.15181430.14192720X-RAY DIFFRACTION100
5.17-24.940.19921530.17372815X-RAY DIFFRACTION99.8

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