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- PDB-3l3q: Mouse importin alpha-pepTM NLS peptide complex -

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Basic information

Entry
Database: PDB / ID: 3l3q
TitleMouse importin alpha-pepTM NLS peptide complex
Components
  • Importin subunit alpha-2
  • pepTM
KeywordsPROTEIN TRANSPORT / ARMADILLO REPEATS
Function / homology
Function and homology information


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 / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / cytoplasmic stress granule ...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 / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / cytoplasmic stress granule / protein import into nucleus / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / nucleus / cytosol
Similarity search - Function
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 ...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
CITRATE ANION / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTakeda, A.A.S. / Kobe, B. / Fontes, M.R.M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Probing the specificity of binding to the major nuclear localization sequence-binding site of importin-alpha using oriented peptide library screening.
Authors: Yang, S.N.Y. / Takeda, A.A.S. / Fontes, M.R.M. / Harris, J.M. / Jans, D.A. / Kobe, B.
History
DepositionDec 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-2
B: pepTM
C: pepTM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0634
Polymers49,8743
Non-polymers1891
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.756, 90.899, 100.968
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 Importin subunit alpha-2 / / Importin alpha-2 / Karyopherin subunit alpha-2 / SRP1-alpha / RAG cohort protein 1 / Pendulin / ...Importin alpha-2 / Karyopherin subunit alpha-2 / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / Importin alpha P1


Mass: 46271.953 Da / Num. of mol.: 1 / Fragment: NLS binding domain (UNP residues 71-497)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P52293
#2: Protein/peptide pepTM


Mass: 1801.031 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence was obtained by an oriented peptide library approach to probe the specificity of the major NLS binding site in importin alpha.
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.62 Å3/Da / Density % sol: 66.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium Citrate, DTT, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.55 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 29414 / Num. obs: 29414 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.094
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.094 / % possible all: 89.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PJN

1pjn


Resolution: 2.3→33.79 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.905 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22662 1500 5.1 %RANDOM
Rwork0.18691 ---
obs0.18891 27893 89.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.563 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 13 107 3510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223460
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9754704
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1215439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83325.507138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.62215609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3931515
X-RAY DIFFRACTIONr_chiral_restr0.1280.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022546
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.21579
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22365
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2114
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0471.52290
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70323572
X-RAY DIFFRACTIONr_scbond_it2.5931343
X-RAY DIFFRACTIONr_scangle_it3.9034.51132
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.298→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 105 -
Rwork0.252 1947 -
obs--85.93 %

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