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- PDB-3ukw: Mouse importin alpha: Bimax1 peptide complex -

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Basic information

Entry
Database: PDB / ID: 3ukw
TitleMouse importin alpha: Bimax1 peptide complex
Components
  • Bimax1 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 / protein import into nucleus / cytoplasmic stress granule / 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 / protein import into nucleus / cytoplasmic stress granule / 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: 2.1 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 ...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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: Importin subunit alpha-2
C: Bimax1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1763
Polymers58,9672
Non-polymers2091
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint7 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.561, 89.493, 99.900
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 Bimax1 peptide


Mass: 3698.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Designed peptide inhibitor
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.8M sodium citrate, 10mM DTT, 0.1M BisTris, 10% glycerol, pH 6.5, 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: 2.1→43.6 Å / Num. obs: 41865 / % possible obs: 76.8 % / 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: 2.1→42.151 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 0 / σ(I): 4.3 / Phase error: 17.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 2056 5.04 %RANDOM
Rwork0.1765 ---
obs0.1777 40755 97.49 %-
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.374 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso max: 94.67 Å2 / Biso mean: 28.8024 Å2 / Biso min: 6.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.3893 Å2-0 Å20 Å2
2---1.0938 Å2-0 Å2
3---1.483 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 14 276 3741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043529
X-RAY DIFFRACTIONf_angle_d0.7894803
X-RAY DIFFRACTIONf_chiral_restr0.055568
X-RAY DIFFRACTIONf_plane_restr0.004614
X-RAY DIFFRACTIONf_dihedral_angle_d13.4361322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14890.24571340.20692460259495
2.1489-2.20260.24611200.19942496261695
2.2026-2.26210.24991320.22412415254793
2.2621-2.32870.25011140.18862447256193
2.3287-2.40390.22291450.16982516266197
2.4039-2.48980.19741330.1622569270298
2.4898-2.58940.19421350.16762584271998
2.5894-2.70730.20071370.16862585272298
2.7073-2.850.17551530.16522534268798
2.85-3.02850.19561210.16622649277099
3.0285-3.26220.20531450.17182616276199
3.2622-3.59040.19541380.170326612799100
3.5904-4.10950.18661520.160826572809100
4.1095-5.17610.16931510.166326912842100
5.1761-42.15990.20381460.204128192965100
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)
10.02950.00360.00610.00390.0050.0067-0.00690.0072-0.01780.0012-0.0046-0.02990.01470.02310.00520.37420.0629-0.03960.18450.03160.38191.9257-16.754115.3629
20.1007-0.0433-0.00530.22920.07880.10450.05-0.016-0.0735-0.09320.00150.01450.0525-0.08920.08520.1580.0289-0.06360.10330.0370.1306-5.591-13.97418.7775
30.00320.0050.00220.12290.04530.01710.02240.0994-0.0375-0.1620.012-0.01690.09420.19310.00050.29830.08170.00310.232-0.00010.1115-4.0708-8.87294.7939
40.10860.07280.0230.12750.00790.01470.1247-0.05080.02090.06190.02290.06740.0683-0.03920.05940.0843-0.0089-0.06540.06190.02880.0301-8.45414.101317.1392
50.5186-0.1027-0.18360.4201-0.0190.07190.00940.07190.12170.1052-0.0137-0.05290.0194-0.01460.01180.0928-0.0105-0.0220.07820.0030.1281-1.646417.729614.6536
60.17850.0362-0.06270.1296-0.00070.05850.04780.06530.08810.0572-0.01030.0583-0.0123-0.0279-0.03510.10080.00110.01610.09640.00360.15233.09326.39199.344
70.20350.0392-0.08210.0586-0.01850.06580.02720.20480.16790.01390.08910.1304-0.0156-0.095-0.02530.07840.00660.03960.09060.08980.1618.131935.822-8.084
80.17390.0541-0.02840.02410.01720.10730.02110.11280.0584-0.04420.08170.08950.0624-0.20150.03610.1748-0.0199-0.08770.34770.17870.16248.035137.2319-24.2293
90.0052-0.02660.05160.1926-0.25820.48110.01670.180.0719-0.16230.06710.02350.22160.03660.03110.45490.05010.05620.73460.22740.295312.587543.6228-31.7785
100.0220.01090.01890.01080.01250.0168-0.03420.03780.0336-0.0724-0.05150.02390.0198-0.0933-0.05220.5129-0.0572-0.24720.81040.09910.2690.669635.7219-35.4875
110.0881-0.02570.01090.0159-0.00260.00190.02030.03960.0205-0.020.05680.06990.0137-0.0541-0.03680.2081-0.01490.01260.27430.14670.316-2.643533.2078-10.4615
120.08070.0435-0.01620.03160.0080.07320.02950.0602-0.0167-0.02420.01190.01620.00260.0048-0.01930.1468-0.02180.0240.16250.00180.17082.39716.1708-2.6362
130.5552-0.04340.37860.28040.20760.5008-0.0409-0.0575-0.0424-0.0269-0.0481-0.0702-0.02220.13490.06010.09650.0059-0.01870.14640.0380.14592.58382.91749.4872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 72:76)B72 - 76
2X-RAY DIFFRACTION2(chain B and resid 77:105)B77 - 105
3X-RAY DIFFRACTION3(chain B and resid 106:117)B106 - 117
4X-RAY DIFFRACTION4(chain B and resid 118:213)B118 - 213
5X-RAY DIFFRACTION5(chain B and resid 214:249)B214 - 249
6X-RAY DIFFRACTION6(chain B and resid 250:314)B250 - 314
7X-RAY DIFFRACTION7(chain B and resid 315:414)B315 - 414
8X-RAY DIFFRACTION8(chain B and resid 415:452)B415 - 452
9X-RAY DIFFRACTION9(chain B and resid 453:473)B453 - 473
10X-RAY DIFFRACTION10(chain B and resid 474:497)B474 - 497
11X-RAY DIFFRACTION11(chain C and resid 5:10)C5 - 10
12X-RAY DIFFRACTION12(chain C and resid 11:19)C11 - 19
13X-RAY DIFFRACTION13(chain C and resid 20:26)C20 - 26

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