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- PDB-7tmx: Structure of Mouse Importin alpha NEIL1 NLS Peptide Complex -

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Basic information

Entry
Database: PDB / ID: 7tmx
TitleStructure of Mouse Importin alpha NEIL1 NLS Peptide Complex
Components
  • Importin subunit alpha-1
  • Nuclear Localization Signal from Endonuclease 8-like 1
KeywordsNUCLEAR PROTEIN / Importin-alpha / Complex / BER / NLS
Function / homology
Function and homology information


negative regulation of nuclease activity / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / Sensing of DNA Double Strand Breaks / DNA N-glycosylase activity / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / NLS-dependent protein nuclear import complex / hydrolase activity, acting on glycosyl bonds ...negative regulation of nuclease activity / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / Sensing of DNA Double Strand Breaks / DNA N-glycosylase activity / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / NLS-dependent protein nuclear import complex / hydrolase activity, acting on glycosyl bonds / postsynapse to nucleus signaling pathway / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / base-excision repair / cytoplasmic stress granule / protein import into nucleus / host cell / chromosome / DNA-binding transcription factor binding / response to oxidative stress / damaged DNA binding / postsynaptic density / centrosome / glutamatergic synapse / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Endonuclease VIII-like 1, DNA binding / Endonuclease VIII-like 1, DNA bind / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Importin subunit alpha ...Endonuclease VIII-like 1, DNA binding / Endonuclease VIII-like 1, DNA bind / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / 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 / Armadillo-like helical / Ribosomal protein S13-like, H2TH / Armadillo-type fold
Similarity search - Domain/homology
Importin subunit alpha-1 / Endonuclease 8-like 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMoraes, I.R. / de Oliveira, H.C. / Fontes, M.R.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP) Brazil
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2023
Title: Structural basis of nuclear transport for NEIL DNA glycosylases mediated by importin-alpha.
Authors: Moraes, I.R. / de Oliveira, H.C. / Fontes, M.R.M.
History
DepositionJan 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Importin subunit alpha-1
A: Nuclear Localization Signal from Endonuclease 8-like 1
B: Nuclear Localization Signal from Endonuclease 8-like 1


Theoretical massNumber of molelcules
Total (without water)54,4103
Polymers54,4103
Non-polymers00
Water1,63991
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)78.541, 90.378, 99.569
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 (E. coli) / References: UniProt: P52293
#2: Protein/peptide Nuclear Localization Signal from Endonuclease 8-like 1 / DNA glycosylase/AP lyase Neil1 / DNA-(apurinic or apyrimidinic site) lyase Neil1 / Endonuclease ...DNA glycosylase/AP lyase Neil1 / DNA-(apurinic or apyrimidinic site) lyase Neil1 / Endonuclease VIII-like 1 / FPG1 / Nei homolog 1 / NEH1 / Nei-like protein 1


Mass: 2261.704 Da / Num. of mol.: 2 / Fragment: Residues 359-378 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q96FI4, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.25 Å3/Da / Density % sol: 62.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium citrate buffer (pH 6.0), sodium citrate and DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.3→39.17 Å / Num. obs: 58874 / % possible obs: 96.97 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.096 / Net I/σ(I): 23.75
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.74 / Num. unique obs: 3006 / CC1/2: 0.76 / % possible all: 95.46

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UL1

3ul1


Resolution: 2.3→39.17 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 2946 5 %
Rwork0.2199 55928 -
obs0.2216 58874 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.3 Å2 / Biso mean: 60.454 Å2 / Biso min: 28.46 Å2
Refinement stepCycle: final / Resolution: 2.3→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3247 0 0 91 3338
Biso mean---52.65 -
Num. residues----437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053312
X-RAY DIFFRACTIONf_angle_d0.744523
X-RAY DIFFRACTIONf_dihedral_angle_d4.826455
X-RAY DIFFRACTIONf_chiral_restr0.042554
X-RAY DIFFRACTIONf_plane_restr0.006581
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.340.34581280.30472510263893
2.34-2.380.35331450.29422721286697
2.38-2.420.27091360.26932647278398
2.42-2.470.31491380.25192701283998
2.47-2.520.29491370.24632709284697
2.52-2.570.28951440.24892705284999
2.57-2.630.27331410.24012690283197
2.63-2.70.23631450.23092710285598
2.7-2.770.24421420.2292701284399
2.77-2.850.25791440.22452683282799
2.85-2.950.27561460.22872720286698
2.95-3.050.25461460.24042705285199
3.05-3.170.24341400.22392708284899
3.17-3.320.2341400.22742749288999
3.32-3.490.28521400.23542709284999
3.49-3.710.39411160.32682334245084
3.71-40.28491350.28232321245685
4-4.40.22261450.17572736288199
4.4-5.040.17671460.159627512897100
5.04-6.340.19371500.191327212871100
6.34-39.170.22721420.14732697283998
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)
11.8676-0.1083-0.95246.93852.7873.31890.2741-0.01490.3167-0.1502-0.12210.0907-0.4758-0.1993-0.14530.2810.02090.02560.2555-0.01260.368346.011392.963765.6663
21.83691.35842.12921.29361.71132.65540.21750.0745-0.350.21450.0022-0.11090.27510.0408-0.21930.3116-0.00880.00720.2437-0.00220.503235.245562.416655.3008
33.2785-1.7107-1.50173.39390.81977.66010.1810.9933-0.3174-0.93990.0818-0.95130.04250.7678-0.23550.54220.00590.10790.7943-0.21560.724432.10550.602824.2643
46.56731.3872-3.16269.94574.25054.02480.52291.51840.2257-0.7622-0.87560.3789-0.7066-0.26340.37420.59670.19450.07790.89580.3191.297537.349386.334658.7299
54.09111.11623.30922.01350.21852.95070.32971.7591-0.4324-1.7842-0.0191-1.7634-0.13610.8852-0.32340.84530.04460.19511.1195-0.25361.153642.014256.320640.5933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 72 through 202 )B72 - 202
2X-RAY DIFFRACTION2chain 'B' and (resid 203 through 390 )B203 - 390
3X-RAY DIFFRACTION3chain 'B' and (resid 391 through 497 )B391 - 497
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 172 )A165 - 172
5X-RAY DIFFRACTION5chain 'C' and (resid 921 through 924 )C921 - 924

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