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- PDB-3knd: TPX2:importin-alpha complex -

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Basic information

Entry
Database: PDB / ID: 3knd
TitleTPX2:importin-alpha complex
Components
  • Importin subunit alpha-2
  • Targeting protein for Xklp2
KeywordsPROTEIN TRANSPORT / mitosis / importin / Transport
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 / activation of protein kinase activity / regulation of mitotic spindle organization ...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 / activation of protein kinase activity / regulation of mitotic spindle organization / spindle pole / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / microtubule / postsynaptic density / cell cycle / cell division / glutamatergic synapse / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
TPX2 / Aurora-A binding / TPX2, C-terminal / TPX2 central domain / Targeting protein for Xklp2 (TPX2) domain / Aurora-A binding / Cell cycle regulated microtubule associated protein / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily ...TPX2 / Aurora-A binding / TPX2, C-terminal / TPX2 central domain / Targeting protein for Xklp2 (TPX2) domain / Aurora-A binding / Cell cycle regulated microtubule associated protein / 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 / Targeting protein for Xklp2-A / Targeting protein for Xklp2-A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsStewart, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Novel binding of the mitotic regulator TPX2 (target protein for Xenopus kinesin-like protein 2) to importin-alpha.
Authors: Giesecke, A. / Stewart, M.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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: Targeting protein for Xklp2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6847
Polymers59,2032
Non-polymers4805
Water4,252236
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-2 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.527, 89.317, 99.273
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 / Karyopherin subunit alpha-2 / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex ...Karyopherin subunit alpha-2 / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / Importin alpha P1


Mass: 49886.633 Da / Num. of mol.: 1 / Fragment: residues 70-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: importin alpha 2, Kpna2, Rch1 / Plasmid: pMW172 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P52293
#2: Protein Targeting protein for Xklp2


Mass: 9316.822 Da / Num. of mol.: 1 / Fragment: residues 270-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: TPX2 / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9I8N0, UniProt: Q6NUF4*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.1-1.2 M ammonium sulphate, 100 mM Tris-Hcl, 10 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9814 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2009 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 2.151→27.85 Å / Num. all: 36138 / Num. obs: 36111 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EYJ

1eyj


Resolution: 2.151→19.712 Å / SU ML: 0.27 / Isotropic thermal model: isotropic / σ(F): 0.94 / Phase error: 21.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 4923 6.77 %
Rwork0.1824 --
obs0.1846 -99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.532 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 169.88 Å2 / Biso mean: 51.189 Å2 / Biso min: 18.49 Å2
Baniso -1Baniso -2Baniso -3
1--3.077 Å2-0 Å20 Å2
2---7.913 Å20 Å2
3---10.99 Å2
Refinement stepCycle: LAST / Resolution: 2.151→19.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 25 236 3641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073459
X-RAY DIFFRACTIONf_angle_d0.9934709
X-RAY DIFFRACTIONf_dihedral_angle_d16.3371257
X-RAY DIFFRACTIONf_chiral_restr0.055563
X-RAY DIFFRACTIONf_plane_restr0.005598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.151-2.17570.32861400.30672206X-RAY DIFFRACTION97
2.1757-2.20120.3161400.29212293X-RAY DIFFRACTION99
2.2012-2.2280.40041740.31942127X-RAY DIFFRACTION95
2.228-2.25620.44591420.41532286X-RAY DIFFRACTION99
2.2562-2.28580.34061440.3292127X-RAY DIFFRACTION94
2.2858-2.31710.25091210.23122353X-RAY DIFFRACTION100
2.3171-2.35020.27811630.20742264X-RAY DIFFRACTION100
2.3502-2.38520.22231320.20962316X-RAY DIFFRACTION100
2.3852-2.42240.2061820.20042223X-RAY DIFFRACTION100
2.4224-2.4620.24371910.1942259X-RAY DIFFRACTION100
2.462-2.50440.25561950.18312205X-RAY DIFFRACTION100
2.5044-2.54980.23871840.1892289X-RAY DIFFRACTION100
2.5498-2.59880.22471680.18262256X-RAY DIFFRACTION100
2.5988-2.65170.2341830.18282253X-RAY DIFFRACTION100
2.6517-2.70920.22071760.17422276X-RAY DIFFRACTION100
2.7092-2.77210.21181790.17162237X-RAY DIFFRACTION100
2.7721-2.84120.21821420.17022281X-RAY DIFFRACTION100
2.8412-2.91780.20821660.16642305X-RAY DIFFRACTION100
2.9178-3.00340.23821400.17892286X-RAY DIFFRACTION100
3.0034-3.09990.19971710.17622257X-RAY DIFFRACTION100
3.0999-3.21030.23371560.18062277X-RAY DIFFRACTION100
3.2103-3.33820.22011710.18612257X-RAY DIFFRACTION100
3.3382-3.48940.18761880.17692246X-RAY DIFFRACTION100
3.4894-3.67220.21771600.1652288X-RAY DIFFRACTION100
3.6722-3.90060.18941610.14882268X-RAY DIFFRACTION100
3.9006-4.19910.15631820.1362266X-RAY DIFFRACTION100
4.1991-4.61680.15531790.12752242X-RAY DIFFRACTION100
4.6168-5.27360.15861800.14472260X-RAY DIFFRACTION100
5.2736-6.60250.20811540.18212289X-RAY DIFFRACTION100
6.6025-19.71250.16771590.14172260X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.67140.4624-0.38151.1030.2910.76520.1749-0.04390.3677-0.2576-0.08980.1973-0.1971-0.03-0.10840.31290.07270.0940.2352-0.0070.231837.042982.64556.4442
21.11160.0097-0.87412.808-0.0012-0.5890.2452-0.0060.01320.0444-0.05630.0268-0.1313-0.0739-0.12640.1892-0.00310.02780.1611-0.00660.0568
30.90830.6987-0.04020.6887-0.27780.51630.14610.0451-0.10130.08460.00630.0901-0.01460.0507-0.08230.2009-0.01080.03490.19090.01920.2461
41.13151.06960.57512.00341.00681.37930.30810.1192-0.46270.0624-0.0973-0.24990.03110.0083-0.20220.1671-0.0008-0.06040.1693-0.02360.3109
51.41260.40691.55281.0910.88981.70270.07670.4002-0.25150.02920.2036-0.48590.02260.2962-0.26440.17160.00710.03020.2838-0.10790.3355
62.91931.0362-0.7542.8053-0.11030.25420.02471.2205-0.3313-1.10190.378-0.10940.17780.1403-0.25590.6117-0.07530.20230.9539-0.29130.3433
72.00738.5621.20376.9364-1.34024.4120.35630.55840.08040.31630.21031.0565-0.72660.5178-0.38270.3536-0.08930.04910.3936-0.32911.0726
82.0481-0.06810.65282.86281.48241.21030.0645-0.2502-0.3723-0.23190.02490.45-0.1063-0.47430.00570.2626-0.0371-0.04470.35380.00070.3521
Refinement TLS groupSelection details: chain B and resid 322:331)

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