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- PDB-3zip: minor-site specific NLS (A58) -

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Basic information

Entry
Database: PDB / ID: 3zip
Titleminor-site specific NLS (A58)
Components
  • A58NLS
  • IMPORTIN SUBUNIT ALPHA-2
KeywordsTRANSPORT PROTEIN / NUCLEAR IMPORT / NUCLEAR LOCALIZATION SIGNALS
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 / host cell / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule ...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 / host cell / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / nuclear membrane / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / nucleus / 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: 2.4 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

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Assembly

Deposited unit
A: IMPORTIN SUBUNIT ALPHA-2
B: A58NLS
C: A58NLS


Theoretical massNumber of molelcules
Total (without water)52,9803
Polymers52,9803
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.140, 90.180, 99.430
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: 49872.836 Da / Num. of mol.: 1 / Fragment: RESIDUES 72-497
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 A58NLS


Mass: 1553.769 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 / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.23 Å3/Da / Density % sol: 61.89 % / Description: NONE
Crystal growpH: 6.5
Details: 0.75 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: 2.4→19.87 Å / Num. obs: 28437 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 52.74 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.1 / % 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: 2.4→19.83 Å / Cor.coef. Fo:Fc: 0.9561 / Cor.coef. Fo:Fc free: 0.9425 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.204 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.162
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.1905 1435 5.05 %RANDOM
Rwork0.1643 ---
obs0.1656 28389 99.99 %-
Displacement parametersBiso mean: 58.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.9631 Å20 Å20 Å2
2--4.2164 Å20 Å2
3----5.1795 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 0 49 3443
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013455HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014700HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1612SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes489HARMONIC5
X-RAY DIFFRACTIONt_it3455HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion3.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion479SEMIHARMONIC5
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_contact4261SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2461 151 5.17 %
Rwork0.1985 2768 -
all0.2009 2919 -
obs--99.99 %
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)
11.8606-0.41861.36546.5694-2.25113.78310.1450.1573-0.1911-0.4499-0.0214-0.28840.26630.2538-0.1235-0.02220.0373-0.0471-0.0942-0.0076-0.0499-5.6006-8.258515.3859
21.85440.92610.42552.6665-0.51650.87340.0849-0.12770.12610.22580.01070.0208-0.0703-0.0528-0.0956-0.03560.0034-0.0028-0.066-0.0044-0.0307-4.863914.833816.4526
32.170.1602-0.64594.211-1.12282.25930.09360.0760.11790.17230.00290.2196-0.21230.0035-0.0965-0.0769-0.00490.0446-0.06580.02770.02933.43428.8265.8779
42.33330.3455-1.07282.8208-0.91332.9099-0.00480.78810.3178-0.42420.17240.3825-0.0567-0.536-0.1676-0.1617-0.0057-0.03760.02730.1517-0.07738.400337.4981-19.2805
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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