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- PDB-5wun: Crystal structure of mouse importin-alpha1 bound to non-phosphory... -

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Basic information

Entry
Database: PDB / ID: 5wun
TitleCrystal structure of mouse importin-alpha1 bound to non-phosphorylated NLS of EBNA1
Components
  • Epstein-Barr nuclear antigen 1Epstein–Barr virus nuclear antigen 1
  • Importin subunit alpha-1
KeywordsPROTEIN TRANSPORT/PEPTIDE / importin / nuclear localization signal / nuclear import / PROTEIN TRANSPORT-PEPTIDE complex
Function / homology
Function and homology information


host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / viral latency / 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 / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / postsynapse to nucleus signaling pathway / enzyme-substrate adaptor activity ...host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / viral latency / 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 / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / postsynapse to nucleus signaling pathway / enzyme-substrate adaptor activity / symbiont-mediated disruption of host cell PML body / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / regulation of DNA replication / host cell / cytoplasmic stress granule / protein import into nucleus / endonuclease activity / DNA-binding transcription factor binding / postsynaptic density / DNA-binding transcription factor activity / virus-mediated perturbation of host defense response / glutamatergic synapse / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / 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 ...Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Epstein-Barr nuclear antigen 1 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Epstein-Barr virus (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsNakada, R. / Hirano, H. / Matsuura, Y.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural basis for the regulation of nuclear import of Epstein-Barr virus nuclear antigen 1 (EBNA1) by phosphorylation of the nuclear localization signal.
Authors: Nakada, R. / Hirano, H. / Matsuura, Y.
History
DepositionDec 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Epstein-Barr nuclear antigen 1
C: Epstein-Barr nuclear antigen 1


Theoretical massNumber of molelcules
Total (without water)51,9793
Polymers51,9793
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint5 kcal/mol
Surface area18430 Å2
Unit cell
Length a, b, c (Å)78.510, 90.180, 98.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 49886.633 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 70-529
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 Epstein-Barr nuclear antigen 1 / Epstein–Barr virus nuclear antigen 1 / EBV nuclear antigen 1


Mass: 1046.159 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 378-386 / Source method: obtained synthetically / Source: (synth.) Epstein-Barr virus (Epstein-Barr virus) / References: UniProt: P03211
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES, sodium citrate, DTT

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→28.8 Å / Num. obs: 36317 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.038 / Rrim(I) all: 0.095 / Net I/σ(I): 14.1 / Num. measured all: 218370 / Scaling rejects: 150
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.2-2.275.20.990.599199.4
9.07-28.85.20.0210.995197.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.5.28data scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UKW

3ukw


Resolution: 2.2→28.8 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.01
RfactorNum. reflection% reflection
Rfree0.2038 1857 5.12 %
Rwork0.1767 --
obs0.178 36258 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.29 Å2 / Biso mean: 48.5728 Å2 / Biso min: 20.55 Å2
Refinement stepCycle: final / Resolution: 2.2→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3340 0 0 174 3514
Biso mean---50.14 -
Num. residues----437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043398
X-RAY DIFFRACTIONf_angle_d0.6834623
X-RAY DIFFRACTIONf_chiral_restr0.04555
X-RAY DIFFRACTIONf_plane_restr0.004592
X-RAY DIFFRACTIONf_dihedral_angle_d2.5032073
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.25950.31581520.27552557270999
2.2595-2.32590.2861270.245826102737100
2.3259-2.4010.29391470.237526092756100
2.401-2.48670.28821460.211426112757100
2.4867-2.58620.26211400.211526372777100
2.5862-2.70390.23731350.202226082743100
2.7039-2.84630.20131550.181826262781100
2.8463-3.02450.21461160.185526632779100
3.0245-3.25770.23351500.176226172767100
3.2577-3.5850.19631350.168726672802100
3.585-4.10240.18391540.147626832837100
4.1024-5.16380.16811530.149226912844100
5.1638-28.80380.16031470.16828222969100

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