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- PDB-3ukx: Mouse importin alpha: Bimax2 peptide complex -

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Basic information

Entry
Database: PDB / ID: 3ukx
TitleMouse importin alpha: Bimax2 peptide complex
Components
  • Bimax2 peptide
  • Importin subunit alpha-2
KeywordsPROTEIN TRANSPORT/INHIBITOR / Arm repeat / Armadillo repeat / Nuclear transport / nuclear localisation signal binding / importin beta binding / PROTEIN TRANSPORT-INHIBITOR complex
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMarfori, M. / Forwood, J.K. / Lonhienne, T.G. / Kobe, B.
CitationJournal: Traffic / Year: 2012
Title: Structural Basis of High-Affinity Nuclear Localization Signal Interactions with Importin-alpha
Authors: Marfori, M. / Lonhienne, T.G. / Forwood, J.K. / Kobe, B.
History
DepositionNov 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

Downloads & links

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Assembly

Deposited unit
B: Importin subunit alpha-2
C: Bimax2 peptide


Theoretical massNumber of molelcules
Total (without water)58,9902
Polymers58,9902
Non-polymers00
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint9 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.187, 90.187, 100.221
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 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: 55268.473 Da / Num. of mol.: 1 / Fragment: UNP Residues 70-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide Bimax2 peptide


Mass: 3721.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Designed peptide inhibitor
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 3.03 Å3/Da / Density % sol: 59.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.75M sodium citrate, 10mM DTT, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953693 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953693 Å / Relative weight: 1
ReflectionResolution: 2.2→43.811 Å / Num. obs: 37159 / % possible obs: 72.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PJN

1pjn


Resolution: 2.2→43.803 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.27 / σ(F): 0 / Phase error: 18.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 1800 4.99 %RANDOM
Rwork0.1777 ---
obs0.1789 36048 97.16 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.845 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 127.4 Å2 / Biso mean: 33.1448 Å2 / Biso min: 9.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.8293 Å2-0 Å20 Å2
2---3.5517 Å2-0 Å2
3---4.381 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 0 316 3778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053532
X-RAY DIFFRACTIONf_angle_d0.8614804
X-RAY DIFFRACTIONf_chiral_restr0.059569
X-RAY DIFFRACTIONf_plane_restr0.004619
X-RAY DIFFRACTIONf_dihedral_angle_d12.3941317
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.25950.31451410.25922431257292
2.2595-2.3260.29141330.23832432256592
2.326-2.4010.23841250.20852558268395
2.401-2.48690.25641260.19932562268896
2.4869-2.58640.22821250.1892600272597
2.5864-2.70410.21551310.18582624275597
2.7041-2.84670.22151520.17432638279099
2.8467-3.0250.20691320.17932673280599
3.025-3.25850.21381470.17782670281799
3.2585-3.58620.20671520.177526922844100
3.5862-4.10480.181480.15512722287099
4.1048-5.17030.15121440.139227422886100
5.1703-43.81180.17011440.178829043048100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.4369-0.0510.35240.24870.04570.40.09320.1274-0.17930.227-0.1475-0.00670.17670.0594-0.04330.2673-0.0518-0.08430.1671-0.01310.1655.6797-16.0007-18.9685
20.389-0.16910.09880.43480.2020.17450.09380.003-0.05440.0095-0.0167-0.02140.1014-0.01820.25130.13960.0038-0.03340.0914-0.00410.07876.91261.8413-15.7083
30.635-0.2493-0.11850.567-0.17310.15430.0025-0.03510.2461-0.1792-0.04680.10050.0620.00640.03960.14630.0109-0.03180.12240.00450.15531.477118.1138-15.1682
40.2365-0.1539-0.24850.21720.11910.26310.1328-0.0170.3122-0.11380.0279-0.1334-0.13780.02210.13530.10470.00840.04820.0858-0.01950.1965-2.988829.0447-8.1236
50.4087-0.1355-0.16320.22890.19340.55170.0571-0.30820.25430.02830.1454-0.2342-0.02620.20790.20190.0934-0.0179-0.00040.1756-0.11020.1838-9.714635.958214.2471
60.6635-0.0682-0.13680.7904-0.01670.03160.0417-0.86720.18360.73080.2781-0.41260.20420.60770.0140.59050.0273-0.13460.9115-0.30830.4189-5.925940.465432.8185
70.0733-0.075-0.16730.08890.3112.1431-0.0482-0.07940.13930.16030.0509-0.10860.4159-0.0345-0.19280.2511-0.0024-0.01680.2882-0.20260.48853.291531.99988.9748
85.10890.05950.81872.43880.32670.17640.1641-0.01740.0627-0.0282-0.1499-0.0440.0263-0.1181-0.00891.1710.31550.02410.9882-0.00480.8178-1.741516.27684.1067
90.3693-0.4128-0.13190.47080.07990.57510.1535-0.00590.09310.1274-0.11490.30740.0549-0.2477-0.03230.137-0.02070.0370.2204-0.01080.2405-2.49494.935-8.8004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 72:94)B72 - 94
2X-RAY DIFFRACTION2(chain B and resid 95:213)B95 - 213
3X-RAY DIFFRACTION3(chain B and resid 214:248)B214 - 248
4X-RAY DIFFRACTION4(chain B and resid 249:335)B249 - 335
5X-RAY DIFFRACTION5(chain B and resid 336:449)B336 - 449
6X-RAY DIFFRACTION6(chain B and resid 450:497)B450 - 497
7X-RAY DIFFRACTION7(chain C and resid 4:12)C4 - 12
8X-RAY DIFFRACTION8(chain C and resid 13:17)C13 - 17
9X-RAY DIFFRACTION9(chain C and resid 18:26)C18 - 26

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