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- PDB-3ul0: Mouse importin alpha: mouse CBP80Y8D cNLS complex -

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Basic information

Entry
Database: PDB / ID: 3ul0
TitleMouse importin alpha: mouse CBP80Y8D 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 / SLBP independent Processing of Histone Pre-mRNAs / FGFR2 alternative splicing / 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 / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Pre-transcription Events ...Formation of the Early Elongation Complex / SLBP independent Processing of Histone Pre-mRNAs / FGFR2 alternative splicing / 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 / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Minor Pathway / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / snRNA export from nucleus / nuclear cap binding complex / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / mRNA Splicing - Major Pathway / positive regulation of mRNA 3'-end processing / cap-dependent translational initiation / : / RNA cap binding / alternative mRNA splicing, via spliceosome / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / regulation of mRNA processing / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / regulatory ncRNA-mediated post-transcriptional gene silencing / positive regulation of viral life cycle / mRNA 3'-end processing / RNA 7-methylguanosine cap binding / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / positive regulation of mRNA splicing, via spliceosome / RNA catabolic process / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / spliceosomal complex assembly / 7-methylguanosine mRNA capping / mRNA export from nucleus / host cell / positive regulation of transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / cytoplasmic stress granule / protein import into nucleus / positive regulation of cell growth / DNA-binding transcription factor binding / defense response to virus / postsynaptic density / molecular adaptor activity / ribonucleoprotein complex / mRNA binding / 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 / MOLECULAR REPLACEMENT / Resolution: 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: Nuclear cap-binding protein subunit 1


Theoretical massNumber of molelcules
Total (without water)58,1732
Polymers58,1732
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint4 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.691, 89.898, 99.792
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: 2904.127 Da / Num. of mol.: 1 / Fragment: mCBP80 cNLS peptide, residues 1-23 / Mutation: Y8D
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 / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 59.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.7M 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: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5419 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2→40.983 Å / Num. obs: 48448 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / % possible all: 99.9

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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: 2→40.983 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.26 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 2348 5.07 %RANDOM
Rwork0.1875 ---
obs0.1886 46290 95.43 %-
all-48448 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.131 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 121.58 Å2 / Biso mean: 36.6675 Å2 / Biso min: 12.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.3823 Å2-0 Å20 Å2
2---4.8204 Å2-0 Å2
3---6.2027 Å2
Refinement stepCycle: LAST / Resolution: 2→40.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 0 330 3768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063529
X-RAY DIFFRACTIONf_angle_d0.9664808
X-RAY DIFFRACTIONf_chiral_restr0.065572
X-RAY DIFFRACTIONf_plane_restr0.005621
X-RAY DIFFRACTIONf_dihedral_angle_d14.3191314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.04080.32321080.23812421252990
2.0408-2.08520.23491440.22662452259692
2.0852-2.13370.29921220.20742482260492
2.1337-2.18710.25241360.20652454259092
2.1871-2.24620.24911310.19752481261293
2.2462-2.31230.20911230.18972504262793
2.3123-2.38690.22571230.19722529265294
2.3869-2.47220.24091220.20182518264094
2.4722-2.57120.23411460.21142539268595
2.5712-2.68820.23391240.21832616274096
2.6882-2.82990.22621490.19742604275397
2.8299-3.00710.23071430.20322630277398
3.0071-3.23920.23541560.19442671282799
3.2392-3.5650.20291400.18942719285999
3.565-4.08050.16611530.161227212874100
4.0805-5.13940.16811620.15162739290199
5.1394-40.9920.19181660.18622862302899
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)
10.03540.0158-0.02670.1379-0.00420.0366-0.0392-0.12260.0524-0.359-0.04340.1282-0.14770.0125-0.00280.38210.05270.08790.3039-0.0330.348144.0793107.232866.2826
20.0510.0259-0.02890.0504-0.01910.0189-0.04280.03720.2023-0.0848-0.09630.1808-0.13170.0473-0.00190.26840.03250.02110.1884-0.03650.215241.821799.909863.6061
30.07440.0642-0.02720.0604-0.01520.02340.176-0.09460.16360.0947-0.0545-0.15460.0094-0.09480.0020.3095-0.01620.05590.2347-0.04710.210550.999396.017269.8367
40.09640.022-0.02310.10430.03680.04230.0884-0.0373-0.02550.031-0.007-0.0298-0.08270.084100.212-0.01270.03070.1947-0.02230.175947.189683.572166.1572
50.0676-0.02330.06520.0212-0.03030.06560.03760.0005-0.11850.1261-0.00210.1624-0.1052-0.00530.00020.2222-0.00130.05360.20380.01920.243738.324873.436566.0286
60.14390.0069-0.00620.03910.00670.09660.06640.0426-0.16410.12180.04010.00650.046-0.02910.01060.1324-0.0099-0.00210.12190.00650.167139.557566.379162.0867
70.03040.04330.01720.07630.04680.04180.14180.0104-0.19450.1047-0.0445-0.18790.08330.0051-0.00120.2109-0.0103-0.04070.2044-0.02150.299635.282860.395657.0043
80.07420.03430.01250.01610.01820.16260.00010.1504-0.21690.12710.1004-0.2322-0.03450.05360.00860.1977-0.0062-0.0480.2135-0.0420.311931.848857.484747.3191
90.12720.13710.0670.19710.02340.13270.05340.3291-0.3107-0.0140.1095-0.3530.08780.19530.01980.23770.0203-0.01590.3088-0.10290.354929.001851.016735.481
100.1629-0.05480.09440.2240.01230.06660.06220.3246-0.076-0.35870.0334-0.1897-0.06710.15980.08860.4549-0.01170.13980.6692-0.22890.288434.141851.054419.4118
110.13160.07240.04120.04040.02860.07740.04140.187-0.2133-0.2361-0.0342-0.02640.1630.0570.01690.4024-0.05560.13650.4505-0.21950.505942.612259.253341.0463
120.0123-0.0028-0.00390.00790.00550.0042-0.02460.075-0.0337-0.0826-0.0068-0.12050.01140.0622-0.00060.3564-0.03480.0190.3628-0.0280.263941.804471.255944.1541
130.0240.01210.00780.00670.00270.004-0.0605-0.0598-0.0601-0.07940.08570.1045-0.0192-0.11070.00010.22350.01480.00690.2464-0.01180.215936.867985.136958.7806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 71:88)B71 - 88
2X-RAY DIFFRACTION2(chain B and resid 89:116)B89 - 116
3X-RAY DIFFRACTION3(chain B and resid 117:133)B117 - 133
4X-RAY DIFFRACTION4(chain B and resid 134:213)B134 - 213
5X-RAY DIFFRACTION5(chain B and resid 214:241)B214 - 241
6X-RAY DIFFRACTION6(chain B and resid 242:281)B242 - 281
7X-RAY DIFFRACTION7(chain B and resid 282:313)B282 - 313
8X-RAY DIFFRACTION8(chain B and resid 314:361)B314 - 361
9X-RAY DIFFRACTION9(chain B and resid 362:427)B362 - 427
10X-RAY DIFFRACTION10(chain B and resid 428:496)B428 - 496
11X-RAY DIFFRACTION11(chain C and resid 1:6)C1 - 6
12X-RAY DIFFRACTION12(chain C and resid 7:13)C7 - 13
13X-RAY DIFFRACTION13(chain C and resid 14:23)C14 - 23

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