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- PDB-6p6a: Structure of Mouse Importin alpha - NIT2 NLS peptide complex -

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Basic information

Entry
Database: PDB / ID: 6p6a
TitleStructure of Mouse Importin alpha - NIT2 NLS peptide complex
Components
  • Importin subunit alpha-1
  • Nitrogen catabolic enzyme regulatory protein
KeywordsTRANSPORT PROTEIN / nuclear import / importin alpha / transcription factor
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / regulation of transcription by glucose / 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 / NLS-bearing protein import into nucleus / nuclear import signal receptor activity / nuclear localization sequence binding / non-canonical NF-kappaB signal transduction ...Sensing of DNA Double Strand Breaks / regulation of transcription by glucose / 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 / NLS-bearing protein import into nucleus / nuclear import signal receptor activity / nuclear localization sequence binding / non-canonical NF-kappaB signal transduction / nitrate assimilation / positive regulation of type I interferon production / histone deacetylase binding / cytoplasmic stress granule / protein import into nucleus / host cell / nuclear membrane / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / postsynaptic density / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of DNA-templated transcription / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Nitrogen regulatory protein areA, GATA-like domain / Nitrogen regulatory protein areA, GATA-like domain / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Importin subunit alpha / Atypical Arm repeat ...Nitrogen regulatory protein areA, GATA-like domain / Nitrogen regulatory protein areA, GATA-like domain / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / 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, NHR/GATA-type / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Nitrogen catabolic enzyme regulatory protein / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Neurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.151 Å
AuthorsBernardes, N.E. / Fukuda, C.A. / Silva, T.D. / 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.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _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

Downloads & links

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Assembly

Deposited unit
B: Importin subunit alpha-1
A: Nitrogen catabolic enzyme regulatory protein
C: Nitrogen catabolic enzyme regulatory protein


Theoretical massNumber of molelcules
Total (without water)53,0403
Polymers53,0403
Non-polymers00
Water5,152286
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)78.678, 90.180, 99.181
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: 49886.633 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 Nitrogen catabolic enzyme regulatory protein / Nitrogen regulatory protein 2 / NIT2


Mass: 1576.805 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
References: UniProt: P19212
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 3.32 Å3/Da / Density % sol: 66.51 %
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: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 2.151→36.57 Å / Num. obs: 38952 / % possible obs: 99.82 % / Redundancy: 12.7 % / Biso Wilson estimate: 33.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1158 / Rpim(I) all: 0.03352 / Rrim(I) all: 0.1206 / Net I/σ(I): 2.28
Reflection shellResolution: 2.151→2.228 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.056 / Mean I/σ(I) obs: 0.819 / Num. unique obs: 3788 / CC1/2: 0.819 / Rpim(I) all: 0.3214 / % possible all: 99.11

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata scaling
PHENIXphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U5P

5u5p


Resolution: 2.151→36.568 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.18
RfactorNum. reflection% reflection
Rfree0.1961 3705 5.02 %
Rwork0.1657 --
obs0.1672 73869 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.28 Å2 / Biso mean: 44.1196 Å2 / Biso min: 18.63 Å2
Refinement stepCycle: final / Resolution: 2.151→36.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 0 286 3610
Biso mean---49.55 -
Num. residues----437
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.151-2.17910.35481320.3132258995
2.1791-2.20890.29731430.27722695100
2.2089-2.24050.3081390.24672698100
2.2405-2.27390.25791430.23352707100
2.2739-2.30940.23121480.2192727100
2.3094-2.34730.24831440.21322690100
2.3473-2.38780.25511450.20592722100
2.3878-2.43120.21551430.19692691100
2.4312-2.47790.21191390.18842693100
2.4779-2.52850.23961430.18052711100
2.5285-2.58340.22121430.1852728100
2.5834-2.64350.20061420.17982663100
2.6435-2.70960.23011420.17152712100
2.7096-2.78290.18161420.15992702100
2.7829-2.86470.22241430.15892716100
2.8647-2.95710.20341360.1572678100
2.9571-3.06280.18251460.16712725100
3.0628-3.18530.22691410.16282705100
3.1853-3.33020.19271440.16352736100
3.3302-3.50570.18941450.16632677100
3.5057-3.72510.18461450.15332729100
3.7251-4.01240.16091370.13222689100
4.0124-4.41560.15331450.12752702100
4.4156-5.05310.16281470.13722713100
5.0531-6.36090.17631500.17422682100
6.3609-36.5680.17621380.1479268499
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)
11.2867-0.1927-0.46862.53121.08510.90880.10880.04640.1221-0.09230.00190.0146-0.1742-0.1145-0.11890.26370.00610.04080.23290.01690.186445.838992.827665.2624
20.95840.72741.04790.9090.79531.54970.09940.0858-0.21270.08230.0168-0.05690.08910.0385-0.1090.20640.0008-0.00180.2102-0.01050.27835.143162.32555.1989
30.9703-0.3328-0.12211.39490.30142.01530.10930.764-0.1897-0.64160.1126-0.39620.02320.488-0.13780.4660.0090.08660.7018-0.16770.444832.180251.049524.0072
43.0858-2.0137-0.47641.86151.2772.0757-0.27290.09670.3261-0.21630.24270.0499-0.14380.71390.0580.4376-0.08110.03670.5515-0.15020.547842.172957.408842.2602
56.00861.29662.3478.5882-1.93428.64280.3614-0.1266-0.4772-0.4547-0.3741.01730.2426-0.14360.00120.24090.0074-0.03050.3053-0.03450.249136.951486.216759.8142
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 129 through 133 )B129 - 133
5X-RAY DIFFRACTION5chain 'C' and (resid 127 through 132 )C127 - 132

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