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- PDB-1q1t: Mouse Importin alpha: non-phosphorylated SV40 CN peptide complex -

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Basic information

Entry
Database: PDB / ID: 1q1t
TitleMouse Importin alpha: non-phosphorylated SV40 CN peptide complex
Components
  • Importin alpha-2 subunit
  • Large T antigen
KeywordsPROTEIN TRANSPORT / importin alpha/karyopherin alpha / nuclear localisation sequence (NLS) recognition / phosphorylation / simian virus (SV40) large tumor-antigen (T-antigen) NLS / X-ray crystal structure
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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / bidirectional double-stranded viral DNA replication / viral DNA genome replication / nuclear import signal receptor activity / DNA 3'-5' helicase ...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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / bidirectional double-stranded viral DNA replication / viral DNA genome replication / nuclear import signal receptor activity / DNA 3'-5' helicase / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / helicase activity / cytoplasmic stress granule / protein import into nucleus / single-stranded DNA binding / host cell / double-stranded DNA binding / DNA-binding transcription factor binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA replication / postsynaptic density / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / glutamatergic synapse / ATP hydrolysis activity / zinc ion binding / nucleoplasm / ATP binding / identical protein 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 / Importin subunit alpha ...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 / 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. / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsFontes, M.R.M. / Teh, T. / Toth, G. / John, A. / Pavo, I. / Jans, D.A. / Kobe, B.
Citation
Journal: Biochem.J. / Year: 2003
Title: Role of flanking sequences and phosphorylation in the recognition of the simian-virus-40 large T-antigen nuclear localization sequences by importin-alpha
Authors: Fontes, M.R.M. / Teh, T. / Toth, G. / John, A. / Pavo, I. / Jans, D.A. / Kobe, B.
#1: 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.M. / Teh, T. / Kobe, B.
History
DepositionJul 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Large T antigen
B: Large T antigen
C: Importin alpha-2 subunit


Theoretical massNumber of molelcules
Total (without water)55,8333
Polymers55,8333
Non-polymers00
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.157, 89.282, 100.335
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 Large T antigen


Mass: 2685.940 Da / Num. of mol.: 2 / Fragment: CN peptide / Mutation: S120A, S123A, T124A / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE IS NATURALLY FOUND IN SIMIAN VIRUS 40 (SV40) LARGE TUMOR-ANTIGEN
References: UniProt: P03070
#2: Protein Importin alpha-2 subunit / Karyopherin alpha-2 subunit / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex ...Karyopherin alpha-2 subunit / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / Importin alpha P1


Mass: 50461.285 Da / Num. of mol.: 1 / Fragment: NLS binding domain (70-529)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: KPNA2 OR RCH1 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / References: UniProt: P03070, UniProt: P52293*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: Sodium Citrate, DTT, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 6.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 mg/mlpeptide1drop
20.7-0.8 Msodium citrate1drop
3100 mMHEPES1reservoirpH6.0-6.5
410 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 13, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. all: 25902 / Num. obs: 25902 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 17.1 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 19.8
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 3.9 / % possible all: 88.6
Reflection
*PLUS
Num. measured all: 443936
Reflection shell
*PLUS
% possible obs: 88.6 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1IAL

1ial


Resolution: 2.5→29.62 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1706 6.9 %RANDOM
Rwork0.202 ---
obs0.202 24804 98.2 %-
all-24804 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.7542 Å2 / ksol: 0.358481 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---7.37 Å20 Å2
3---7.55 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 0 302 3710
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 289 7.1 %
Rwork0.239 3792 -
obs-4001 98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16

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