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- PDB-2ynr: mImp_alphadIBB_B54NLS -

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Basic information

Entry
Database: PDB / ID: 2ynr
TitlemImp_alphadIBB_B54NLS
Components
  • B54NLS
  • IMPORTIN SUBUNIT ALPHA
KeywordsTRANSPORT PROTEIN / NUCLEAR LOCALIZATION SIGNAL
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 / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / 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 / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / cytoplasmic stress granule / protein import into nucleus / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / host cell nucleus / nucleoplasm / nucleus / cytosol / cytoplasm
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 / Importin subunit alpha
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChang, C.-W. / Counago, R.L.M. / Williams, S.J. / Boden, M. / Kobe, B.
CitationJournal: Plant Cell / Year: 2012
Title: Crystal Structure of Rice Importin-Alpha and Structural Basis of its Interaction with Plant-Specific Nuclear Localization Signals.
Authors: Chang, C.-W. / Counago, R.L.M. / Williams, S.J. / Boden, M. / Kobe, B.
History
DepositionOct 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 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
B: B54NLS
C: B54NLS


Theoretical massNumber of molelcules
Total (without water)52,6643
Polymers52,6643
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint4.3 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.120, 90.350, 97.130
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 /


Mass: 49842.809 Da / Num. of mol.: 1 / Fragment: NLS BINDING DOMAIN, RESIDUES 72-496
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET30A_MIMPALPHA_DIBB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q52L97, UniProt: P52293*PLUS
#2: Protein/peptide B54NLS


Mass: 1410.753 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PGEX2T-B54NLS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.4 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 6.5
Details: 0.4-0.9 M SODIUM CITRATE, 0.1 M HEPES BUFFER (PH 6.5-8.0) AND 10 MM DTT

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.3→20.1 Å / Num. obs: 30886 / % possible obs: 99.2 % / Observed criterion σ(I): 2.3 / Redundancy: 5 % / Biso Wilson estimate: 44.39 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.1
Reflection shellResolution: 2.3→3.42 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % 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: 2.3→19.81 Å / Cor.coef. Fo:Fc: 0.9185 / Cor.coef. Fo:Fc free: 0.9035 / SU R Cruickshank DPI: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.225 / SU Rfree Blow DPI: 0.184 / SU Rfree Cruickshank DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 1552 5.03 %RANDOM
Rwork0.1997 ---
obs0.2012 30842 99.07 %-
Displacement parametersBiso mean: 60.17 Å2
Baniso -1Baniso -2Baniso -3
1--12.0979 Å20 Å20 Å2
2---4.9738 Å20 Å2
3---17.0718 Å2
Refine analyzeLuzzati coordinate error obs: 0.332 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 0 106 3451
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013402HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.064624HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1593SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes481HARMONIC5
X-RAY DIFFRACTIONt_it3402HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion3.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion472SEMIHARMONIC5
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_contact4169SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.221 147 4.9 %
Rwork0.2014 2855 -
all0.2024 3002 -
obs--99.07 %
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)
12.50573.0213.50415.89791.17277.38860.04570.1413-0.0294-0.70180.0537-0.25030.51070.1915-0.0993-0.22490.1102-0.2016-0.50680.05180.6158-3.569-17.496913.7142
203.1885-2.638412.5636-6.77788.55890.17720.12730.1426-0.1846-0.33370.1098-0.1951-0.47840.1565-0.35280.055-0.1688-0.4107-0.01470.3895-7.8005-15.343323.6614
30.68940.64264.2122.6713-3.23224.73460.14950.5242-0.1532-0.7882-0.1093-0.41780.22130.5126-0.0402-0.20880.1147-0.0135-0.2846-0.0540.5745-0.7204-8.72078.5618
48.2088-1.8981-1.04686.5455-4.03873.39530.0731-0.0364-0.4116-0.15060.16550.34910.20080.0193-0.2386-0.45650.0028-0.1114-0.53050.04750.4306-11.7622-6.877816.3164
54.9345-1.79812.04345.7864-2.5760.25470.1993-0.01010.08070.1196-0.1256-0.17920.01170.4763-0.0736-0.3709-0.0127-0.0551-0.4352-0.02320.6744-4.7236-2.04116.4019
62.65760.53461.21262.9142-0.41961.16850.1163-0.1580.07770.1939-0.0067-0.06130.0334-0.0661-0.1096-0.4515-0.0008-0.013-0.42430.00070.4089-5.03210.675617.2325
711.25933.3915-0.19215.07471.73112.5983-0.07350.36540.3249-0.17060.18240.1889-0.3455-0.1317-0.1089-0.42940.0394-0.0194-0.40620.09550.4636-10.428522.6718.4528
80.15452.545-0.12242.73570.39395.13850.1179-0.0220.42460.0601-0.0589-0.0852-0.15120.1386-0.059-0.4299-0.0254-0.1075-0.4489-0.00080.54465.269722.974116.4345
91.8911.2567-0.21244.4319-1.54312.13950.0370.00440.03480.2989-0.04620.0581-0.12740.06890.0092-0.4968-0.01120.0224-0.42920.01830.50873.281627.81896.8057
1011.402-0.0935-0.13381.0909-3.18532.97880.16570.12820.51090.0768-0.03260.2469-0.4179-0.2228-0.1332-0.36990.01250.083-0.34970.12160.75320.562536.23381.3242
116.82980.0798-1.81123.14-2.02951.42480.0260.2107-0.37790.3268-0.0828-0.10680.1544-0.30180.0568-0.4586-0.03340.0414-0.35650.07270.431512.768130.5803-3.0566
125.0935-0.4751-3.42661.075-1.36442.8630.20380.44130.59880.11610.03420.261-0.2648-0.2571-0.238-0.4776-0.00150.0325-0.37580.070.53159.857639.9204-7.8633
132.2055-0.4093-3.13813.1823-0.51442.36020.02120.116-0.1922-0.1421-0.01810.09790.3809-0.5053-0.0031-0.4184-0.0827-0.0415-0.24570.01260.69969.954526.3322-16.3288
140.65652.5829-1.5841.42732.23280.69280.07240.812-0.3058-0.16320.02210.2843-0.5123-0.7445-0.0946-0.4943-0.0063-0.0315-0.15250.14850.49595.031941.6906-14.9458
1503.4549-7.53083.8492-0.56142.0381-0.01570.49020.17440.0646-0.0624-0.0013-0.3944-0.00650.078-0.3950.05850.0002-0.22720.19080.733114.070547.7329-15.8784
1601.26751.01860.10711.8518.306-0.03480.4829-0.1555-0.4556-0.05690.09990.2882-0.20980.0918-0.38-0.0125-0.0592-0.09970.00910.581711.099333.1993-25.2244
177.56082.19272.27930.28082.40527.49620.030.70260.2424-0.5085-0.04260.0926-0.3035-0.94420.0126-0.62290.0681-0.1597-0.07080.18830.21794.324243.2842-24.0369
181.5683.1794-0.19280.9555-0.03520.4343-0.00970.14920.215-0.11950.0277-0.0145-0.17590.1193-0.018-0.324-0.0522-0.01790.14080.08960.241914.554146.3268-31.3549
1901.46522.97731.081-0.54724.139-0.00790.0575-0.1275-0.1457-0.00490.15770.1251-0.02910.01290.1434-0.0934-0.08870.2449-0.0168-0.14565.027334.0985-35.4688
201.54240.6575.40870.65860.09851.85250.02670.1992-0.0143-0.3319-0.0365-0.07720.0579-0.19130.0098-0.21950.1332-0.62820.2961-0.00690.1028-1.963239.4769-32.9458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 72 - 85
2X-RAY DIFFRACTION2CHAIN A AND RESID 86 - 95
3X-RAY DIFFRACTION3CHAIN A AND 96 - 116
4X-RAY DIFFRACTION4CHAIN A AND RESID 117 - 130
5X-RAY DIFFRACTION5CHAIN A AND RESID 131 - 153
6X-RAY DIFFRACTION6CHAIN A AND RESID 154 - 236
7X-RAY DIFFRACTION7CHAIN A AND RESID 237 - 251
8X-RAY DIFFRACTION8CHAIN A AND RESID 252 - 268
9X-RAY DIFFRACTION9CHAIN A AND RESID 269 - 314
10X-RAY DIFFRACTION10CHAIN A AND RESID 315 - 330
11X-RAY DIFFRACTION11CHAIN A AND RESID 331 - 355
12X-RAY DIFFRACTION12CHAIN A AND RESID 356 - 387
13X-RAY DIFFRACTION13CHAIN A AND RESID 388 - 396
14X-RAY DIFFRACTION14CHAIN A AND RESID 397 - 410
15X-RAY DIFFRACTION15CHAIN A AND RESID 411 - 419
16X-RAY DIFFRACTION16CHAIN A AND RESID 420 - 433
17X-RAY DIFFRACTION17CHAIN A AND RESID 434 - 456
18X-RAY DIFFRACTION18CHAIN A AND RESID 457 - 467
19X-RAY DIFFRACTION19CHAIN A AND RESID 468 - 480
20X-RAY DIFFRACTION20CHAIN A AND RESID 481 - 494

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