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- PDB-3ul1: Mouse importin alpha: nucleoplasmin cNLS peptide complex -

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Basic information

Entry
Database: PDB / ID: 3ul1
TitleMouse importin alpha: nucleoplasmin cNLS peptide complex
Components
  • Importin subunit alpha-2
  • Nucleoplasmin
KeywordsPROTEIN TRANSPORT/NUCLEAR PROTEIN / Arm repeat / Armadillo repeat / Nuclear transport / nuclear localisation signal binding / importin beta binding / PROTEIN TRANSPORT-NUCLEAR PROTEIN complex
Function / homology
Function and homology information


sperm DNA decondensation / histone chaperone activity / 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 / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding ...sperm DNA decondensation / histone chaperone activity / 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 / importin-alpha family protein binding / 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 / nucleosome binding / positive regulation of DNA replication / cytoplasmic stress granule / protein import into nucleus / host cell / histone binding / DNA-binding transcription factor binding / postsynaptic density / chromatin remodeling / glutamatergic synapse / nucleolus / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / 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 ...Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / 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
Nucleoplasmin / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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
A: Nucleoplasmin


Theoretical massNumber of molelcules
Total (without water)57,5582
Polymers57,5582
Non-polymers00
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-1 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.156, 90.094, 99.332
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 Nucleoplasmin


Mass: 2289.762 Da / Num. of mol.: 1 / Fragment: Nucleoplasmin cNLS peptide, residues 153-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P05221
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.79M sodium citrate, 10mM DTT, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5419 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.9→42.07 Å / Num. obs: 55684 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.9→1.97 Å / % possible all: 93.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine: 1.7_650)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PJN

1pjn


Resolution: 1.9→42.07 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.31 / σ(F): 0 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 2659 5.08 %RANDOM
Rwork0.1914 ---
obs0.193 52372 92.46 %-
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.998 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 131.79 Å2 / Biso mean: 39.9733 Å2 / Biso min: 15.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.5476 Å2-0 Å20 Å2
2---7.176 Å2-0 Å2
3---7.7236 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 0 292 3692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053501
X-RAY DIFFRACTIONf_angle_d0.8864776
X-RAY DIFFRACTIONf_chiral_restr0.06577
X-RAY DIFFRACTIONf_plane_restr0.005611
X-RAY DIFFRACTIONf_dihedral_angle_d13.361305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.93460.42141080.36332090219875
1.9346-1.97180.3631160.32232260237681
1.9718-2.0120.30451230.26712324244784
2.012-2.05580.27241290.23752415254486
2.0558-2.10360.25231490.22742487263689
2.1036-2.15620.24681410.20962508264990
2.1562-2.21450.23751320.2112564269691
2.2145-2.27970.26711400.20312636277694
2.2797-2.35320.24061220.20652654277694
2.3532-2.43730.3161420.20832623276594
2.4373-2.53490.23131500.19852619276994
2.5349-2.65030.26211230.20962720284395
2.6503-2.790.20551620.20222717287997
2.79-2.96470.2541300.1992765289597
2.9647-3.19360.2211530.19872798295198
3.1936-3.51480.24981560.19342827298399
3.5148-4.0230.17851510.16712842299399
4.023-5.06720.17151590.14472868302799
5.0672-42.08070.19711730.18162996316999
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)
10.08050.15060.2780.55150.43970.9891-0.21710.4685-0.4768-0.98510.5004-0.30790.11120.5321-0.15540.37520.00650.01880.4911-0.22660.513542.231754.60139.0872
22.7076-1.1507-0.86320.68430.99123.0206-0.27-0.18330.1745-1.2143-0.0566-0.4031-0.4937-0.0227-0.12010.4967-0.03110.0880.2173-0.01520.378238.587572.145947.1377
31.36620.2771-1.08792.6348-0.84322.9095-0.20080.034-0.5199-0.22390.04960.76730.5481-0.49360.03690.11770.0297-0.01550.29870.00760.258536.730887.246959.7649
40.95971.1905-0.45927.04541.95181.35140.1521-0.17540.4793-1.2761-0.20960.3323-0.5245-0.0223-0.06580.46160.07920.17420.2864-0.01560.306245.2567107.30265.795
51.21150.4299-0.21721.25910.0570.32450.04830.29990.2328-0.3925-0.06430.2202-0.242-0.3078-0.01740.36160.05320.01480.29490.00080.239842.5672100.13762.8107
60.7414-0.0853-0.17242.40820.25020.02560.0585-0.070.00260.09910.0436-0.1378-0.04610.057-0.03830.226-0.00870.02010.2218-0.01880.155647.894685.725366.8238
71.39320.22050.89341.5134-0.24570.7610.10980.0483-0.15220.1875-0.06160.0927-0.1404-0.05180.01150.2343-0.01440.01280.19240.01390.216641.03771.939864.7748
81.16311.15910.52531.37460.43121.85170.11670.0562-0.1980.1541-0.0232-0.18020.15270.0418-0.05160.112-0.016-0.02290.10430.01130.162636.916763.375860.2619
91.67921.05350.78260.84251.02541.7180.07560.2304-0.24260.01580.1248-0.39370.06770.1594-0.09310.19940.0166-0.01980.2222-0.06410.296430.835555.670942.9353
101.70110.35790.55190.0880.08181.3593-0.00080.63-0.4507-0.28260.2899-0.41160.01070.42920.32410.3516-0.03360.09150.5138-0.21330.375530.98351.587126.8776
111.7930.49050.39520.9782-0.02310.1448-0.14671.4302-0.4124-1.26510.5444-0.6458-0.05830.83551.4910.725-0.12340.24071.0998-0.41040.436833.699849.30416.7368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 152:157)A152 - 157
2X-RAY DIFFRACTION2(chain A and resid 158:165)A158 - 165
3X-RAY DIFFRACTION3(chain A and resid 166:172)A166 - 172
4X-RAY DIFFRACTION4(chain B and resid 72:88)B72 - 88
5X-RAY DIFFRACTION5(chain B and resid 89:117)B89 - 117
6X-RAY DIFFRACTION6(chain B and resid 118:213)B118 - 213
7X-RAY DIFFRACTION7(chain B and resid 214:249)B214 - 249
8X-RAY DIFFRACTION8(chain B and resid 250:307)B250 - 307
9X-RAY DIFFRACTION9(chain B and resid 308:410)B308 - 410
10X-RAY DIFFRACTION10(chain B and resid 411:450)B411 - 450
11X-RAY DIFFRACTION11(chain B and resid 451:497)B451 - 497

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