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- PDB-4u54: IMPORTIN-ALPHA MINOR NLS SITE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 4u54
TitleIMPORTIN-ALPHA MINOR NLS SITE INHIBITOR
ComponentsImportin subunit alpha-1
KeywordsTRANSPORT PROTEIN / TPX2 inhibitor
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 / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding ...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 / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / 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
N-methyl-1-[3-(pyridin-3-yl)phenyl]methanamine / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.41 Å
AuthorsStewart, M. / Valkov, E. / Holvey, R.S.
CitationJournal: Chemmedchem / Year: 2015
Title: Selective Targeting of the TPX2 Site of Importin-alpha Using Fragment-Based Ligand Design.
Authors: Holvey, R.S. / Valkov, E. / Neal, D. / Stewart, M. / Abell, C.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2May 8, 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: Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2832
Polymers46,0851
Non-polymers1981
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.424, 91.298, 98.816
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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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: 46084.805 Da / Num. of mol.: 1 / Fragment: UNP residues 74-498
Source method: isolated from a genetically manipulated source
Details: deltaIBB / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Chemical ChemComp-3C5 / N-methyl-1-[3-(pyridin-3-yl)phenyl]methanamine


Mass: 198.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: See publication for details. Precipitant was 1.05-1.2 M ammonium sulphate, 0.1M citrate pH 6.0, 20-40 mM DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2011 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.41→20 Å / Num. obs: 27498 / % possible obs: 98.4 % / Redundancy: 4.3 % / Net I/σ(I): 11
Reflection shellResolution: 2.41→2.5 Å / Mean I/σ(I) obs: 2.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: dev_1702)refinement
XSCALEdata reduction
RefinementResolution: 2.41→20.033 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 1384 5.04 %
Rwork0.1859 --
obs0.1879 27455 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.81 Å2 / Biso mean: 49.0226 Å2 / Biso min: 25.38 Å2
Refinement stepCycle: final / Resolution: 2.41→20.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 15 121 3376
Biso mean--54.51 47.64 -
Num. residues----425

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