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- PDB-5x8n: Crystal structure of mouse importin-alpha1 bound to the nuclear l... -

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Basic information

Entry
Database: PDB / ID: 5x8n
TitleCrystal structure of mouse importin-alpha1 bound to the nuclear localization signal of Epstein-Barr virus EBNA-LP protein
Components
  • Epstein-Barr nuclear antigen leader protein
  • Importin subunit alpha-1
KeywordsPROTEIN TRANSPORT/TRANSCRIPTION / importin / NLS / EBNA-LP / Epstein-Barr virus / PROTEIN TRANSPORT-TRANSCRIPTION complex
Function / homology
Function and homology information


host cell PML body / DNA-templated viral transcription / 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 / symbiont-mediated disruption of host cell PML body / nuclear import signal receptor activity ...host cell PML body / DNA-templated viral transcription / 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 / symbiont-mediated disruption of host cell PML body / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / nuclear membrane / DNA-binding transcription factor binding / postsynaptic density / transcription coactivator activity / glutamatergic synapse / host cell nucleus / nucleoplasm / nucleus / cytosol
Similarity search - Function
Herpesvirus leader protein / Herpesvirus leader protein / 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. ...Herpesvirus leader protein / Herpesvirus leader protein / 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
Importin subunit alpha-1 / Epstein-Barr nuclear antigen leader protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsNakada, R. / Matsuura, Y.
CitationJournal: Protein Sci. / Year: 2017
Title: Crystal structure of importin-alpha bound to the nuclear localization signal of Epstein-Barr virus EBNA-LP protein
Authors: Nakada, R. / Matsuura, Y.
History
DepositionMar 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
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

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Assembly

Deposited unit
A: Importin subunit alpha-1
B: Epstein-Barr nuclear antigen leader protein


Theoretical massNumber of molelcules
Total (without water)52,5942
Polymers52,5942
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint3 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.270, 90.290, 98.170
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 leader protein / EBV nuclear antigen leader protein / Epstein-Barr nuclear antigen 5 / EBV nuclear antigen 5


Mass: 2707.118 Da / Num. of mol.: 1 / Fragment: UNP residues 29-50 / Source method: obtained synthetically
Source: (synth.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8))
References: UniProt: Q8AZK7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / 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: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→30.77 Å / Num. obs: 38548 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 38.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.039 / Rrim(I) all: 0.095 / Net I/σ(I): 13.1 / Num. measured all: 227759 / Scaling rejects: 138
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.15-2.225.80.9640.680.4361.06100
8.86-30.7750.0340.9990.0170.03898.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.5.31data scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
Cootmodel building
Aimlessdata processing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WUM

5wum


Resolution: 2.15→30.765 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.99
RfactorNum. reflection% reflection
Rfree0.2099 1896 4.93 %
Rwork0.1852 --
obs0.1865 38484 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.49 Å2 / Biso mean: 48.2742 Å2 / Biso min: 22.18 Å2
Refinement stepCycle: final / Resolution: 2.15→30.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3316 0 0 123 3439
Biso mean---48.63 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033374
X-RAY DIFFRACTIONf_angle_d0.6564593
X-RAY DIFFRACTIONf_chiral_restr0.04554
X-RAY DIFFRACTIONf_plane_restr0.004587
X-RAY DIFFRACTIONf_dihedral_angle_d2.632056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.15-2.20380.31161240.271625732697
2.2038-2.26330.28511380.243925652703
2.2633-2.32990.27471250.232225822707
2.3299-2.40510.26941320.226125752707
2.4051-2.4910.24761470.203425792726
2.491-2.59070.24021420.207725712713
2.5907-2.70850.24361360.198226012737
2.7085-2.85120.22961300.184526002730
2.8512-3.02970.21271330.194426182751
3.0297-3.26340.23031190.195226182737
3.2634-3.59140.18481190.187126462765
3.5914-4.110.17851500.165226292779
4.11-5.17420.17851440.1626532797
5.1742-30.76820.20331570.169927782935

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