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- PDB-5wum: Crystal structure of mouse importin-alpha1 bound to S385-phosphor... -

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Basic information

Entry
Database: PDB / ID: 5wum
TitleCrystal structure of mouse importin-alpha1 bound to S385-phosphorylated NLS of EBNA1
Components
  • Epstein-Barr 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 / viral latency / Sensing of DNA Double Strand Breaks / regulation of transcription by glucose / 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 / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / NLS-bearing protein import into nucleus ...host cell PML body / viral latency / Sensing of DNA Double Strand Breaks / regulation of transcription by glucose / 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 / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / NLS-bearing protein import into nucleus / nuclear import signal receptor activity / symbiont-mediated disruption of host cell PML body / nuclear localization sequence binding / non-canonical NF-kappaB signal transduction / regulation of DNA replication / enzyme-substrate adaptor activity / positive regulation of type I interferon production / histone deacetylase binding / protein import into nucleus / cytoplasmic stress granule / host cell / endonuclease activity / nuclear membrane / DNA-binding transcription factor binding / symbiont-mediated suppression of host NF-kappaB cascade / postsynaptic density / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / glutamatergic synapse / DNA binding / nucleoplasm / nucleus / cytoplasm / 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 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)52,1393
Polymers52,1393
Non-polymers00
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint5 kcal/mol
Surface area18910 Å2
Unit cell
Length a, b, c (Å)77.910, 90.300, 99.630
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
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 / EBV nuclear antigen 1


Mass: 1126.138 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


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.36 Å3/Da / Density % sol: 63.4 %
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: May 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→41.97 Å / Num. obs: 48181 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 33.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Rrim(I) all: 0.065 / Net I/σ(I): 19 / Num. measured all: 288684 / Scaling rejects: 116
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.054.80.8630.653199.3
8.94-41.975.20.0151199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.5.8data scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UKW

3ukw


Resolution: 2→39.065 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.18
RfactorNum. reflection% reflection
Rfree0.2115 2434 5.06 %
Rwork0.1859 --
obs0.1872 48111 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.67 Å2 / Biso mean: 43.4774 Å2 / Biso min: 19.07 Å2
Refinement stepCycle: final / Resolution: 2→39.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 0 258 3621
Biso mean---48.47 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043422
X-RAY DIFFRACTIONf_angle_d0.634658
X-RAY DIFFRACTIONf_chiral_restr0.038558
X-RAY DIFFRACTIONf_plane_restr0.004596
X-RAY DIFFRACTIONf_dihedral_angle_d2.8152089
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.04080.33041310.28212639277099
2.0408-2.08520.29551420.250526062748100
2.0852-2.13370.27321530.237926542807100
2.1337-2.18710.26461310.222826732804100
2.1871-2.24620.2321440.210526402784100
2.2462-2.31230.2631270.203626872814100
2.3123-2.38690.25121520.205226502802100
2.3869-2.47220.28181370.193926622799100
2.4722-2.57120.22441500.197626662816100
2.5712-2.68810.22961370.203227082845100
2.6881-2.82980.19781600.18926462806100
2.8298-3.00710.22741230.193927102833100
3.0071-3.23910.23911450.193126912836100
3.2391-3.56490.20291400.178827032843100
3.5649-4.08030.17811550.156127182873100
4.0803-5.13890.17231590.160227422901100
5.1389-39.0720.18791480.178128823030100

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