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- PDB-1iq1: CRYSTAL STRUCTURE OF THE IMPORTIN-ALPHA(44-54)-IMPORTIN-ALPHA(70-... -

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Basic information

Entry
Database: PDB / ID: 1iq1
TitleCRYSTAL STRUCTURE OF THE IMPORTIN-ALPHA(44-54)-IMPORTIN-ALPHA(70-529) COMPLEX
Components(IMPORTIN ALPHA-2 SUBUNIT) x 2
KeywordsPROTEIN TRANSPORT / armadillo repeat / solenoid / autoinhibition
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
Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsCatimel, B. / Teh, T. / Fontes, M.R.M. / Jennings, I.G. / Kobe, B.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Biophysical characterization of interactions involving importin-alpha during nuclear import.
Authors: Catimel, B. / Teh, T. / Fontes, M.R. / Jennings, I.G. / Jans, D.A. / Howlett, G.J. / Nice, E.C. / Kobe, B.
History
DepositionMay 28, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IMPORTIN ALPHA-2 SUBUNIT
B: IMPORTIN ALPHA-2 SUBUNIT
C: IMPORTIN ALPHA-2 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)52,6163
Polymers52,6163
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.939, 89.623, 100.372
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 IMPORTIN ALPHA-2 SUBUNIT


Mass: 1364.552 Da / Num. of mol.: 2 / Fragment: AUTOINHIBITORY PEPTIDE(RESIDUES 44-54) / Source method: obtained synthetically / Details: peptide synthesis / References: UniProt: P52293
#2: Protein IMPORTIN ALPHA-2 SUBUNIT


Mass: 49886.633 Da / Num. of mol.: 1 / Fragment: ARMADILLO REPEAT DOMAIN(RESIDUES 70-529)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium phosphate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: unknown / Details: Fontes, M.R.M., (2000) J. Mol. Biol., 297, 1183.
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: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1999
RadiationMonochromator: Mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 17671 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.9
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.3 / % possible all: 96.9
Reflection
*PLUS
Num. obs: 18165 / % possible obs: 97.6 % / Num. measured all: 142209
Reflection shell
*PLUS
% possible obs: 96.9 %

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Processing

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

1ial


Resolution: 2.8→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.248 850 5 %
Rwork0.209 --
all-18116 -
obs-17671 97.6 %
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati sigma a0.47 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 0 95 3472
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.335 --
Rwork0.315 --
obs-2755 97.8 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rfree: 0.335 / Rfactor Rwork: 0.315 / Rfactor obs: 0.315

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