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- PDB-5xzx: Crystal structure of importin-alpha3 bound to the nuclear localiz... -

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Basic information

Entry
Database: PDB / ID: 5xzx
TitleCrystal structure of importin-alpha3 bound to the nuclear localization signal of Ran-binding protein 3
Components
  • Importin subunit alpha-3
  • Ran-binding protein 3
KeywordsTRANSPORT PROTEIN / nuclear import
Function / homology
Function and homology information


dopamine secretion / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / R-SMAD binding / nuclear pore / protein export from nucleus / ISG15 antiviral mechanism ...dopamine secretion / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / R-SMAD binding / nuclear pore / protein export from nucleus / ISG15 antiviral mechanism / small GTPase binding / protein import into nucleus / gene expression / nuclear membrane / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat ...Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / 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 / PH-like domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-3 / Ran-binding protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKoyama, M. / Matsuura, Y.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of importin-alpha 3 bound to the nuclear localization signal of Ran-binding protein 3
Authors: Koyama, M. / Matsuura, Y.
History
DepositionJul 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin subunit alpha-3
B: Ran-binding protein 3


Theoretical massNumber of molelcules
Total (without water)48,9912
Polymers48,9912
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-4 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.970, 60.220, 85.020
Angle α, β, γ (deg.)90.000, 100.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Importin subunit alpha-3 / / Importin alpha Q1 / Qip1 / Karyopherin subunit alpha-4


Mass: 45761.113 Da / Num. of mol.: 1 / Fragment: UNP residues 70-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA4, QIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00629
#2: Protein/peptide Ran-binding protein 3 / RanBP3-b


Mass: 3230.351 Da / Num. of mol.: 1 / Fragment: UNP residues 31-60
Source method: isolated from a genetically manipulated source
Details: This is a fragment of isoform 3 of Ran-binding protein 3, also known as RanBP3-b.
Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H6Z4

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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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 8000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→48.86 Å / Num. obs: 9597 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 75.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.034 / Rrim(I) all: 0.064 / Net I/σ(I): 12 / Num. measured all: 33080 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3-3.183.50.2680.9770.1680.31899.6
9-48.863.30.0220.9990.0140.02694.5

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UAE

4uae


Resolution: 3→37.13 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.8
RfactorNum. reflection% reflection
Rfree0.2807 435 4.55 %
Rwork0.2266 --
obs0.2292 9560 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 206.9 Å2 / Biso mean: 101.0576 Å2 / Biso min: 43.43 Å2
Refinement stepCycle: final / Resolution: 3→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 0 0 3304
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023365
X-RAY DIFFRACTIONf_angle_d0.5024596
X-RAY DIFFRACTIONf_chiral_restr0.037555
X-RAY DIFFRACTIONf_plane_restr0.004598
X-RAY DIFFRACTIONf_dihedral_angle_d1.9762052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0003-3.43420.3061350.29923021315699
3.4342-4.32560.3011650.24763027319299
4.3256-37.13250.25961350.19633077321298
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)
10.59520.6786-0.4061-0.2076-1.15971.21060.1122-0.04750.29390.01130.4531-0.0762-0.4143-0.213600.83830.2217-0.01890.7607-0.09911.01-18.176227.718511.5894
21.2415-0.31190.44781.54870.47710.6211-0.0922-0.16180.31-0.10120.1797-0.06140.1313-0.102200.49410.023-0.0120.56280.05090.726-15.806612.03429.847
33.0251-0.47240.68670.39070.12651.8274-0.133-0.1881-0.32940.10650.0629-0.0319-0.0962-0.0505-00.51390.0125-0.01440.53890.13140.5855-1.3378-1.522410.4312
40.3003-0.21090.47310.1989-0.01790.3838-0.1403-0.11360.29240.12970.33251.22410.26390.148100.5908-0.03690.10630.57490.18430.623813.0941-2.142112.3845
51.507-0.50691.10810.76740.41410.50020.0919-0.18550.29780.21860.17440.09430.29310.101600.68460.08510.0910.67850.26690.510918.0697-10.330721.9939
60.89730.11310.65650.6609-0.88710.59630.3578-0.24770.05560.9045-0.23230.1123-0.1804-0.141401.12360.10860.02231.08050.15130.510625.0375-9.147934.6247
70.42390.74350.42840.42520.44960.12231.4382-1.578-0.2134-0.2655-0.3662-0.0769-0.0169-0.20601.8107-0.02760.09351.69850.2710.962522.414-14.399743.3678
8-0.1364-0.37110.0194-0.129-0.18660.05450.9303-0.82230.31031.8432-0.5124-0.79470.464-0.385501.8923-0.0780.01171.98170.02011.203324.4104-10.943851.7664
90.0204-0.028-0.0278-0.0355-0.02380.0941-0.2397-1.17510.06210.5373-0.58750.0501-0.29860.034300.34190.1505-0.06740.3312-0.14020.40531.653510.029618.5971
10-0.07080.05420.02990.0145-0.2337-0.0368-0.59210.1673-0.1343-0.63730.2841-0.62190.10490.7543-00.69550.0299-0.15440.58230.02751.3128-4.064322.09078.9384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 72:120)A72 - 120
2X-RAY DIFFRACTION2(chain A and resid 121:201)A121 - 201
3X-RAY DIFFRACTION3(chain A and resid 202:283)A202 - 283
4X-RAY DIFFRACTION4(chain A and resid 284:307)A284 - 307
5X-RAY DIFFRACTION5(chain A and resid 308:371)A308 - 371
6X-RAY DIFFRACTION6(chain A and resid 372:422)A372 - 422
7X-RAY DIFFRACTION7(chain A and resid 423:447)A423 - 447
8X-RAY DIFFRACTION8(chain A and resid 448:485)A448 - 485
9X-RAY DIFFRACTION9(chain B and resid 46:52)B46 - 52
10X-RAY DIFFRACTION10(chain B and resid 53:59)B53 - 59

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