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- PDB-3uky: Mouse importin alpha: yeast CBP80 cNLS complex -

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Basic information

Entry
Database: PDB / ID: 3uky
TitleMouse importin alpha: yeast CBP80 cNLS complex
Components
  • Importin subunit alpha-2
  • Nuclear cap-binding protein complex subunit 1
KeywordsPROTEIN TRANSPORT/PROTEIN BINDING / Arm repeat / Armadillo repeat / Nuclear transport / nuclear localisation signal binding / importin beta binding / PROTEIN TRANSPORT-PROTEIN BINDING complex
Function / homology
Function and homology information


Processing of Intronless Pre-mRNAs / nuclear cap binding complex / Sensing of DNA Double Strand Breaks / RNA cap binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / entry of viral genome into host nucleus through nuclear pore complex via importin / primary miRNA processing / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway ...Processing of Intronless Pre-mRNAs / nuclear cap binding complex / Sensing of DNA Double Strand Breaks / RNA cap binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / entry of viral genome into host nucleus through nuclear pore complex via importin / primary miRNA processing / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / mRNA 3'-end processing / commitment complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear import signal receptor activity / response to osmotic stress / Processing of Capped Intron-Containing Pre-mRNA / Formation of the Early Elongation Complex / mRNA Capping / RNA Polymerase II Pre-transcription Events / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / nuclear-transcribed mRNA catabolic process / 7-methylguanosine mRNA capping / mRNA export from nucleus / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / protein import into nucleus / cytoplasmic stress granule / host cell / DNA-binding transcription factor binding / postsynaptic density / mRNA binding / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / nucleus / cytosol
Similarity search - Function
MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Importin subunit alpha / Atypical Arm repeat ...MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / 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
Nuclear cap-binding protein complex subunit 1 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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: Nuclear cap-binding protein complex subunit 1


Theoretical massNumber of molelcules
Total (without water)59,3502
Polymers59,3502
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint3 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.195, 89.747, 98.510
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 Nuclear cap-binding protein complex subunit 1 / Cap-binding protein 80 / CBP80


Mass: 4081.608 Da / Num. of mol.: 1 / Fragment: yCBP80 cNLS peptide, residues 1-30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: CBP80 / Production host: Escherichia coli (E. coli) / References: UniProt: P34160
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.8M sodium citrate, 10mM DTT, 0.1M HEPES, pH 7.0, 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: 2.35→50.57 Å / Num. obs: 29432 / % possible obs: 68.4 % / 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: 2.35→43.18 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.29 / σ(F): 0 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1437 5.07 %RANDOM
Rwork0.188 ---
obs0.1894 28351 95.96 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.981 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 237.8 Å2 / Biso mean: 38.6603 Å2 / Biso min: 9.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.6669 Å2-0 Å20 Å2
2---6.3126 Å2-0 Å2
3---6.9795 Å2
Refinement stepCycle: LAST / Resolution: 2.35→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 0 212 3590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023451
X-RAY DIFFRACTIONf_angle_d0.5964696
X-RAY DIFFRACTIONf_chiral_restr0.043561
X-RAY DIFFRACTIONf_plane_restr0.003604
X-RAY DIFFRACTIONf_dihedral_angle_d12.4391283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.4340.25921220.25022392251486
2.434-2.53140.32951300.25452510264091
2.5314-2.64660.3051310.24082560269193
2.6466-2.78610.27141620.22372605276795
2.7861-2.96070.24051310.20082722285398
2.9607-3.18920.22431420.19712743288598
3.1892-3.510.21081610.19562770293199
3.51-4.01760.18831490.169427902939100
4.0176-5.06050.16381490.143728472996100
5.0605-43.18680.18931600.17429753135100
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)
10.0923-0.20030.07190.5357-0.24960.5183-0.3472-0.2171-0.09230.3648-0.20740.64670.1964-0.5727-0.03430.5799-0.24460.05170.2067-0.02880.4601-2.0265-16.9729-13.895
21.1462-0.18780.31321.01080.03670.61870.174-0.0961-0.24710.2889-0.05850.01260.2623-0.0316-0.01450.2378-0.0369-0.03720.173-0.00530.20925.518-11.6778-13.6378
30.5963-0.00880.09760.91250.2601-0.37360.080.01720.0321-0.0567-0.05320.00930.03540.0272-0.010.15840.0145-0.02370.1119-0.01520.13476.96735.8289-17.7704
40.388-0.6258-0.24720.62490.51260.59830.0467-0.04480.0933-0.0699-0.0186-0.0485-0.01050.0166-0.03560.0829-0.00530.00470.0801-0.00410.1746-0.982823.4357-11.1454
51.4569-0.6441-0.84690.25450.30651.42630.0366-0.15840.1961-0.06050.1268-0.2515-0.08550.10830.09210.1071-0.00710.0090.0888-0.04770.223-8.348835.587.0825
60.50170.0444-0.18470.27310.15210.3497-0.031-0.95520.47570.17010.1292-0.0939-0.00920.2382-0.06630.22620.0175-0.07150.4135-0.08830.2837-7.922137.358523.3107
72.3278-0.52820.4262.83051.43651.2219-0.6766-1.83790.3051.17510.99720.0804-0.40220.0477-0.1050.5442-0.0679-0.0560.6944-0.2660.3997-11.75146.099229.9622
81.0004-0.64760.06291.2081-0.0827-0.00160.2854-0.88570.02651.31080.3231-0.68590.37991.0173-0.10610.81340.0382-0.3031.1879-0.09650.5476-0.202237.546734.4157
90.27290.22970.07860.60550.16860.28520.0601-0.0288-0.7994-0.21160.1713-0.07280.91950.3915-0.08470.6160.05380.11160.4302-0.17140.58242.753630.99286.827
101.6173-0.14571.22192.0945-0.18531.42570.30710.1082-0.178-0.0812-0.25960.78480.185-0.2326-0.09190.3291-0.0522-0.00090.2971-0.09060.3104-2.74122.8751-9.5607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 71:78)B71 - 78
2X-RAY DIFFRACTION2(chain B and resid 79:123)B79 - 123
3X-RAY DIFFRACTION3(chain B and resid 124:220)B124 - 220
4X-RAY DIFFRACTION4(chain B and resid 221:310)B221 - 310
5X-RAY DIFFRACTION5(chain B and resid 311:414)B311 - 414
6X-RAY DIFFRACTION6(chain B and resid 415:449)B415 - 449
7X-RAY DIFFRACTION7(chain B and resid 450:472)B450 - 472
8X-RAY DIFFRACTION8(chain B and resid 473:497)B473 - 497
9X-RAY DIFFRACTION9(chain C and resid 3:23)C3 - 23
10X-RAY DIFFRACTION10(chain C and resid 24:30)C24 - 30

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