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- PDB-3zio: minor-site specific NLS (A28) -

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Basic information

Entry
Database: PDB / ID: 3zio
Titleminor-site specific NLS (A28)
Components
  • A28NLS
  • IMPORTIN SUBUNIT ALPHA-2
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding ...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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / cytosol
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChang, C.-W. / Counago, R.M. / Williams, S.J. / Kobe, B.
CitationJournal: Traffic / Year: 2013
Title: Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-Alpha
Authors: Chang, C.-W. / Counago, R.M. / Williams, S.J. / Boden, M. / Kobe, B.
History
DepositionJan 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMPORTIN SUBUNIT ALPHA-2
B: A28NLS
C: A28NLS


Theoretical massNumber of molelcules
Total (without water)52,5003
Polymers52,5003
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-0.1 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.940, 90.180, 100.700
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 / ALPHA_IBB


Mass: 49872.836 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52293
#2: Protein/peptide A28NLS


Mass: 1313.530 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 3.26 Å3/Da / Density % sol: 62.28 % / Description: NONE
Crystal growpH: 6.5
Details: 0.65 M SODIUM CITRATE, 0.1 M HEPES BUFFER (PH 6.5) AND 10 MM DTT

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorDate: Sep 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→19.8 Å / Num. obs: 42561 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 32.71 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IAL

1ial


Resolution: 2.1→19.74 Å / Cor.coef. Fo:Fc: 0.9458 / Cor.coef. Fo:Fc free: 0.9413 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.137 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.123
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2143 5.04 %RANDOM
Rwork0.1825 ---
obs0.1835 42506 99.84 %-
Displacement parametersBiso mean: 38.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.4585 Å20 Å20 Å2
2--3.2027 Å20 Å2
3----2.7443 Å2
Refine analyzeLuzzati coordinate error obs: 0.276 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3373 0 0 142 3515
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013421HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.984651HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1594SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes88HARMONIC2
X-RAY DIFFRACTIONt_gen_planes486HARMONIC5
X-RAY DIFFRACTIONt_it3421HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.39
X-RAY DIFFRACTIONt_other_torsion2.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion473SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4232SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2413 167 5.42 %
Rwork0.2189 2914 -
all0.2201 3081 -
obs--99.84 %
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)
10.9439-0.03240.72095.2141-2.12773.8950.15390.0554-0.1571-0.4171-0.0291-0.16220.19610.289-0.1248-0.05560.0356-0.0615-0.1307-0.0148-0.0517-5.4991-8.246315.5457
21.57670.31540.47391.8619-0.4250.78220.1121-0.06980.0810.1799-0.01480.021-0.00260.0153-0.0972-0.0577-0.0110.001-0.0953-0.0127-0.0029-4.737814.843616.6464
31.81070.3184-0.82112.8572-1.42462.57480.16440.11380.19010.1615-0.05160.2017-0.12080.0642-0.1128-0.0966-0.01150.0575-0.11990.01220.05933.615128.83976.1203
41.80480.5085-1.07932.8286-0.63432.22360.02360.64780.2932-0.45980.17080.433-0.0892-0.5052-0.1945-0.16110.0073-0.04350.00130.1427-0.05018.681637.5397-19.0085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|72 - 156}
2X-RAY DIFFRACTION2{A|157 - 262}
3X-RAY DIFFRACTION3{A|263 - 329}
4X-RAY DIFFRACTION4{A|330 - 497}

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