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- PDB-3ukz: Mouse importin alpha: mouse CBP80 cNLS complex -

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Basic information

Entry
Database: PDB / ID: 3ukz
TitleMouse importin alpha: mouse CBP80 cNLS complex
Components
  • Importin subunit alpha-2
  • Nuclear cap-binding protein 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


Formation of the Early Elongation Complex / FGFR2 alternative splicing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Processing of Intronless Pre-mRNAs / Formation of RNA Pol II elongation complex / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA ...Formation of the Early Elongation Complex / FGFR2 alternative splicing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Processing of Intronless Pre-mRNAs / Formation of RNA Pol II elongation complex / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Pre-transcription Events / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNA export from nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / nuclear cap binding complex / histone mRNA metabolic process / mRNA metabolic process / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / mRNA Splicing - Major Pathway / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / positive regulation of mRNA 3'-end processing / cap-dependent translational initiation / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / alternative mRNA splicing, via spliceosome / primary miRNA processing / miRNA-mediated post-transcriptional gene silencing / positive regulation of viral life cycle / regulatory ncRNA-mediated post-transcriptional gene silencing / RNA 7-methylguanosine cap binding / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / positive regulation of mRNA splicing, via spliceosome / mRNA 3'-end processing / regulation of translational initiation / nuclear import signal receptor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / spliceosomal complex assembly / 7-methylguanosine mRNA capping / mRNA export from nucleus / positive regulation of transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / protein import into nucleus / cytoplasmic stress granule / host cell / positive regulation of cell growth / DNA-binding transcription factor binding / defense response to virus / postsynaptic density / ribonucleoprotein complex / glutamatergic synapse / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm
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
Importin subunit alpha-1 / Nuclear cap-binding protein subunit 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 subunit 1


Theoretical massNumber of molelcules
Total (without water)58,2212
Polymers58,2212
Non-polymers00
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint6 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.943, 90.023, 100.497
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 subunit 1 / Cap-binding protein 80 / CBP80


Mass: 2952.213 Da / Num. of mol.: 1 / Fragment: mCBP80 cNLS peptide, residues 1-23
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cbp80 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3UYV9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.82M 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: 2.3→44.99 Å / Num. obs: 32538 / % possible obs: 72.8 % / 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: 2.3→42.39 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / Phase error: 17.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1603 5.04 %RANDOM
Rwork0.1763 ---
obs0.1778 31818 97.95 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.887 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 125.92 Å2 / Biso mean: 27.8817 Å2 / Biso min: 5.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.7519 Å2-0 Å20 Å2
2---2.6499 Å2-0 Å2
3---3.4018 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 0 307 3755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053509
X-RAY DIFFRACTIONf_angle_d0.7844772
X-RAY DIFFRACTIONf_chiral_restr0.052567
X-RAY DIFFRACTIONf_plane_restr0.004614
X-RAY DIFFRACTIONf_dihedral_angle_d13.4011294
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.37440.28821270.21932626275395
2.3744-2.45920.24111640.19632644280896
2.4592-2.55770.21791380.17892665280397
2.5577-2.6740.22791400.17152678281897
2.674-2.8150.20741510.17492734288598
2.815-2.99130.2191340.17082757289199
2.9913-3.22220.22321510.1752754290599
3.2222-3.54630.20341410.17612794293599
3.5463-4.05910.19541560.17592739289598
4.0591-5.11270.15841440.148428563000100
5.1127-42.3970.21081570.19022968312599
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)
10.00920.0043-0.00560.0055-0.00570.0064-0.0079-0.0122-0.00620.0336-0.01920.04060.008-0.0160.01120.3418-0.0843-0.01540.19090.00280.2259-1.6618-16.6368-15.1276
20.04270.0103-0.00060.0081-0.00480.05080.073-0.0249-0.06340.0451-0.0143-0.00710.04050.01470.06070.1407-0.0233-0.11590.0212-0.0681-0.00896.4417-10.027-16.8068
30.016-0.0134-0.00210.01540.0038-0.00060.0498-0.01090.0124-0.0337-0.00560.00240.02170.01180.03940.11430.0019-0.0360.0684-0.02330.02767.89534.9544-15.2447
40.2916-0.0334-0.02220.19370.02160.24070.0666-0.0192-0.0069-0.09940.03460.06360.0208-0.00940.03080.08390.0007-0.02040.0790.01780.08812.492417.251-16.7094
50.0187-0.0272-0.04820.1312-0.00090.18150.0698-0.01970.163-0.07830.0484-0.0911-0.0335-0.0115-0.01110.0501-0.00310.01590.0723-0.01450.1194-2.238727.6859-8.3256
60.14190.04990.16750.04870.0370.23730.0922-0.0880.1251-0.06050.0381-0.1119-0.02660.02160.02630.06430.00940.0460.0615-0.03460.1458-10.80935.07986.6389
70.0159-0.024-0.00470.03830.00680.00250.0216-0.04090.0528-0.00140.0278-0.0461-0.02240.05930.02520.1079-0.01570.00680.1531-0.18310.1639-9.815139.327318.0379
80.02430.00560.00890.00620.01130.02020.0116-0.02470.01050.00930.0072-0.01290.02910.0267-0.0070.21170.0048-0.080.3247-0.15980.2392-4.319635.67125.1705
90.00060.003-0.00380.0142-0.00040.01950.005-0.08460.04730.05760.0349-0.02280.0669-0.0117-0.01830.542-0.03420.00070.6316-0.20920.287-12.442544.995631.1963
100.0541-0.0038-0.0260.005-0.0060.0266-0.0095-0.04730.01150.0436-0.0273-0.00970.00840.0296-0.00030.54940.0759-0.22980.8249-0.1620.4137-0.523636.582135.1183
110.0199-0.0113-0.02180.00640.01250.0241-0.0021-0.00540.00150.009-0.0058-0.00230.00730.00740.00140.37670.0558-0.03870.4373-0.07080.38942.9229.17798.1759
120.0167-0.0126-0.00150.0338-0.00210.00060.0001-0.00080.0073-0.0023-0.01-0.00610.0026-0.00640.00170.21650.0588-0.00420.1876-0.00810.14213.196919.59897.0999
130.0193-0.0097-0.02270.05830.05380.06190.0011-0.0113-0.00650.00360.01060.0018-0.00140.0077-0.00450.10290.0071-0.01580.0827-0.02010.0952-0.659910.6668-4.1978
140.06660.01840.02230.02790.01040.0456-0.00070.02210.0032-0.0051-0.00070.0091-0.010.00660.00120.138-0.0235-0.00170.1829-0.00330.1094-5.0485-0.5647-13.2068
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 79:135)B79 - 135
3X-RAY DIFFRACTION3(chain B and resid 136:202)B136 - 202
4X-RAY DIFFRACTION4(chain B and resid 203:246)B203 - 246
5X-RAY DIFFRACTION5(chain B and resid 247:327)B247 - 327
6X-RAY DIFFRACTION6(chain B and resid 328:391)B328 - 391
7X-RAY DIFFRACTION7(chain B and resid 392:427)B392 - 427
8X-RAY DIFFRACTION8(chain B and resid 428:451)B428 - 451
9X-RAY DIFFRACTION9(chain B and resid 452:472)B452 - 472
10X-RAY DIFFRACTION10(chain B and resid 473:497)B473 - 497
11X-RAY DIFFRACTION11(chain C and resid 2:6)C2 - 6
12X-RAY DIFFRACTION12(chain C and resid 7:11)C7 - 11
13X-RAY DIFFRACTION13(chain C and resid 12:18)C12 - 18
14X-RAY DIFFRACTION14(chain C and resid 19:23)C19 - 23

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