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- PDB-1ejl: MOUSE IMPORTIN ALPHA-SV40 LARGE T ANTIGEN NLS PEPTIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ejl
TitleMOUSE IMPORTIN ALPHA-SV40 LARGE T ANTIGEN NLS PEPTIDE COMPLEX
Components
  • IMPORTIN ALPHA
  • SV40 LARGE T ANTIGEN NLS PEPTIDE
KeywordsPROTEIN BINDING / importin alpha/karyopherin alpha / nuclear localization sequence (NLS) recognition / simian virus (SV40) large T-antigen
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / 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 / bidirectional double-stranded viral DNA replication / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / viral DNA genome replication / DNA 3'-5' helicase / nuclear import signal receptor activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / 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 / bidirectional double-stranded viral DNA replication / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / viral DNA genome replication / DNA 3'-5' helicase / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / DNA unwinding involved in DNA replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / helicase activity / cytoplasmic stress granule / protein import into nucleus / host cell / double-stranded DNA binding / single-stranded DNA binding / DNA-binding transcription factor binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / postsynaptic density / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / hydrolase activity / virus-mediated perturbation of host defense response / glutamatergic synapse / host cell nucleus / nucleoplasm / ATP binding / identical protein binding / nucleus / 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 / Helicase, superfamily 3, DNA virus ...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 / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / 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. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Large T antigen / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsFontes, M.R. / Teh, T. / Kobe, B.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-alpha.
Authors: Fontes, M.R. / Teh, T. / Kobe, B.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: Autoinhibition by an Internal Nuclear Localization Signal Revealed by the Crystal Structure of Mammalian Importin Alpha
Authors: Kobe, B.
History
DepositionMar 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: SV40 LARGE T ANTIGEN NLS PEPTIDE
B: SV40 LARGE T ANTIGEN NLS PEPTIDE
I: IMPORTIN ALPHA


Theoretical massNumber of molelcules
Total (without water)51,6633
Polymers51,6633
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.228, 89.858, 99.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide SV40 LARGE T ANTIGEN NLS PEPTIDE


Mass: 888.174 Da / Num. of mol.: 2
Fragment: NLS (NUCLEAR LOCALIZATION SIGNAL) MONOPARTITE PEPTIDE, RESIDUES 126-132
Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of this peptide is naturally found in simian virus 40 T antigen (SV40).
References: UniProt: P03070
#2: Protein IMPORTIN ALPHA / KARYOPHERIN ALPHA


Mass: 49886.633 Da / Num. of mol.: 1 / Fragment: NLS-BINDING DOMAIN, RESIDUES 70-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / References: UniProt: P52293

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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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium citrate, Hepes, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.55 Msodium citrate11
2100 mMHEPES11
310 mMdithiothreitol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Aug 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 126036 / Num. obs: 17900 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 71.8 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.742 / Num. unique all: 1669 / % possible all: 95.6
Reflection
*PLUS
Num. measured all: 126036
Reflection shell
*PLUS
% possible obs: 95.6 % / Num. unique obs: 1669 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1353257.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: protein_rep.param
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1611 9.7 %RANDOM (10%)
Rwork0.215 ---
all0.215 16610 --
obs0.215 16610 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.53 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso mean: 41.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.68 Å20 Å20 Å2
2---6.71 Å20 Å2
3---10.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 0 0 3368
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.412 128 7.7 %
Rwork0.333 1539 -
obs--94.7 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Rfactor Rfree: 0.412 / % reflection Rfree: 7.7 % / Rfactor Rwork: 0.333 / Rfactor obs: 0.333

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