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- PDB-6p6e: Structure of Mouse Importin alpha - PAC3 NLS peptide complex -

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Basic information

Entry
Database: PDB / ID: 6p6e
TitleStructure of Mouse Importin alpha - PAC3 NLS peptide complex
Components
  • Importin subunit alpha-1
  • PAC3 NLS
KeywordsTRANSPORT PROTEIN / nuclear import / importin alpha / transcription factor
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 / cytoplasmic stress granule / protein import into nucleus ...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 / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / 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 / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Uncharacterized protein / Importin subunit alpha-1 / pH-response transcription factor pacc-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Neurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsBernardes, N.E. / Silva, T.D. / Fukuda, C.A. / Oliveira, H.C. / Fontes, M.R.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/24705-3 Brazil
CitationJournal: Sci Rep / Year: 2020
Title: Comparative study of the interactions between fungal transcription factor nuclear localization sequences with mammalian and fungal importin-alpha.
Authors: Bernardes, N.E. / Fukuda, C.A. / da Silva, T.D. / de Oliveira, H.C. / de Barros, A.C. / Dreyer, T.R. / Bertolini, M.C. / Fontes, M.R.M.
History
DepositionJun 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 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-1
B: PAC3 NLS
C: PAC3 NLS


Theoretical massNumber of molelcules
Total (without water)55,7833
Polymers55,7833
Non-polymers00
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.490, 90.495, 99.716
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Importin subunit alpha-1 / 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: 49824.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P52293
#2: Protein/peptide PAC3 NLS


Mass: 2979.313 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Neurospora crassa (fungus) / References: UniProt: A0A0B0E960, UniProt: Q7RVQ8*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 3.17 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium Citrate, DTT, ph 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.425 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.99→43.669 Å / Num. obs: 49103 / % possible obs: 99.81 % / Redundancy: 13 % / Biso Wilson estimate: 37.81 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1177 / Rpim(I) all: 0.03373 / Rrim(I) all: 0.1225 / Net I/σ(I): 18.29
Reflection shellResolution: 1.99→2.065 Å / Num. unique obs: 93402 / CC1/2: 0.799 / Rpim(I) all: 0.7203 / % possible all: 98.78

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UKW

3ukw


Resolution: 1.99→43.669 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.75
RfactorNum. reflection% reflection
Rfree0.1966 1915 3.9 %
Rwork0.1749 --
obs0.1755 49068 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.51 Å2 / Biso mean: 47.3455 Å2 / Biso min: 20.79 Å2
Refinement stepCycle: final / Resolution: 1.99→43.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 0 0 312 3639
Biso mean---51.7 -
Num. residues----438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9933-2.04310.38471340.345326398
2.0431-2.09840.32561340.30083317100
2.0984-2.16010.2821350.25183332100
2.1601-2.22980.2491360.21673320100
2.2298-2.30950.17931360.19343345100
2.3095-2.4020.21211350.19033358100
2.402-2.51130.21911350.1843335100
2.5113-2.64370.22171370.1843361100
2.6437-2.80930.19311350.1753353100
2.8093-3.02620.19181380.17123371100
3.0262-3.33060.19131370.17523399100
3.3306-3.81230.17391370.1593379100
3.8123-4.80210.15721400.13713450100
4.8021-43.6690.1971460.1663357099
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)
11.4212-0.63720.80066.1587-2.17711.66880.18980.0501-0.1083-0.135-0.0668-0.01450.20130.1334-0.12210.28160.0099-0.03950.3056-0.0080.2235-6.5083-2.497815.9177
21.07281.0137-1.29091.1072-1.11852.02020.11770.09090.21590.12430.02140.0633-0.1042-0.0404-0.14270.26570.01140.00670.29660.00350.37594.175428.03255.5609
32.0061-0.68330.10193.64240.1263.15760.16471.00980.133-0.99840.0240.6425-0.0569-0.6118-0.10810.54180.0282-0.13290.84340.16020.50616.94738.9535-25.8785
42.3540.5021-0.66754.17165.30857.86930.18750.2003-0.2461-0.63080.0759-0.7554-0.31090.062-0.26730.39870.081-0.00230.5309-0.03660.46811.70524.96258.2707
50.642-1.75541.51434.8008-4.14093.5719-0.44420.2609-0.3389-0.3617-0.57580.61710.3888-1.05380.93660.5733-0.1169-0.05250.54480.10730.7478-2.739532.4262-7.7705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 202 )A72 - 202
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 390 )A203 - 390
3X-RAY DIFFRACTION3chain 'A' and (resid 391 through 497 )A391 - 497
4X-RAY DIFFRACTION4chain 'B' and (resid 297 through 303 )B297 - 303
5X-RAY DIFFRACTION5chain 'C' and (resid 298 through 302 )C298 - 302

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