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- PDB-7jk7: Crystal structure of Importin alpha 2 in complex with LSD1 NLS S1... -

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Basic information

Entry
Database: PDB / ID: 7jk7
TitleCrystal structure of Importin alpha 2 in complex with LSD1 NLS S111E mutant
Components
  • Importin subunit alpha-1
  • Lysine-specific histone demethylase 1A
KeywordsPROTEIN TRANSPORT / Importin alpha demethylase nuclear localisation
Function / homology
Function and homology information


guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / protein demethylase activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / 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 / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity ...guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / protein demethylase activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / 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 / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / NLS-dependent protein nuclear import complex / neuron maturation / muscle cell development / postsynapse to nucleus signaling pathway / positive regulation of neural precursor cell proliferation / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MRF binding / regulation of androgen receptor signaling pathway / DNA repair complex / nuclear import signal receptor activity / nuclear androgen receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of double-strand break repair via homologous recombination / positive regulation of neuroblast proliferation / DNA repair-dependent chromatin remodeling / positive regulation of stem cell proliferation / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone methyltransferase complex / histone demethylase activity / positive regulation of cell size / positive regulation of epithelial to mesenchymal transition / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / epigenetic regulation of gene expression / cellular response to cAMP / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / HDACs deacetylate histones / promoter-specific chromatin binding / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / positive regulation of neuron projection development / cerebral cortex development / protein modification process / cytoplasmic stress granule / protein import into nucleus / p53 binding / cellular response to UV / transcription corepressor activity / flavin adenine dinucleotide binding / host cell / regulation of protein localization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor binding / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / oxidoreductase activity / chromosome, telomeric region / postsynaptic density / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / glutamatergic synapse / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Histone lysine-specific demethylase / SWIRM domain / SWIRM domain / SWIRM domain profile. / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / : ...Histone lysine-specific demethylase / SWIRM domain / SWIRM domain / SWIRM domain profile. / 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 / Amine oxidase / Flavin containing amine oxidoreductase / Armadillo/beta-catenin-like repeats / Armadillo / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / Armadillo-like helical / Armadillo-type fold / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Lysine-specific histone demethylase 1A / Importin subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsTu, W.J. / McCuaig, R. / Tan, A.H.Y. / Hardy, K. / Seddiki, N. / Ali, S. / Dahlstron, J.E. / Bean, E.G. / Dunn, J. / Forwood, J.K. ...Tu, W.J. / McCuaig, R. / Tan, A.H.Y. / Hardy, K. / Seddiki, N. / Ali, S. / Dahlstron, J.E. / Bean, E.G. / Dunn, J. / Forwood, J.K. / Tsimbalyuk, S. / Smith, K.M. / Yip, D. / Malik, L. / Prasana, T. / Milburn, P. / Rao, S.
CitationJournal: Front Immunol / Year: 2020
Title: Targeting Nuclear LSD1 to Reprogram Cancer Cells and Reinvigorate Exhausted T Cells via a Novel LSD1-EOMES Switch.
Authors: Tu, W.J. / McCuaig, R.D. / Tan, A.H.Y. / Hardy, K. / Seddiki, N. / Ali, S. / Dahlstrom, J.E. / Bean, E.G. / Dunn, J. / Forwood, J. / Tsimbalyuk, S. / Smith, K. / Yip, D. / Malik, L. / ...Authors: Tu, W.J. / McCuaig, R.D. / Tan, A.H.Y. / Hardy, K. / Seddiki, N. / Ali, S. / Dahlstrom, J.E. / Bean, E.G. / Dunn, J. / Forwood, J. / Tsimbalyuk, S. / Smith, K. / Yip, D. / Malik, L. / Prasanna, T. / Milburn, P. / Rao, S.
History
DepositionJul 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Lysine-specific histone demethylase 1A
B: Importin subunit alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5266
Polymers54,1572
Non-polymers3684
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-3 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.320, 78.630, 89.540
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/peptide Lysine-specific histone demethylase 1A / BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2 / ...BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2 / [histone H3]-dimethyl-L-lysine(4) FAD-dependent demethylase 1A


Mass: 3186.563 Da / Num. of mol.: 1 / Mutation: S111E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Production host: Escherichia coli (E. coli)
References: UniProt: O60341, [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase
#2: 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: 50970.754 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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.7 M sodium citrate, 0.01M DTT, 0.1M sodium HEPES pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9357 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9357 Å / Relative weight: 1
ReflectionResolution: 1.9→41.684 Å / Num. obs: 48384 / % possible obs: 96.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Net I/σ(I): 13.5
Reflection shellResolution: 1.96→1.96 Å / Rmerge(I) obs: 1.236 / Num. unique obs: 3645 / CC1/2: 0.583

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BVT

6bvt


Resolution: 1.96→41.684 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 2436 5.04 %
Rwork0.1812 45911 -
obs0.1825 48347 95.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.14 Å2 / Biso mean: 52.9818 Å2 / Biso min: 25.56 Å2
Refinement stepCycle: final / Resolution: 1.96→41.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 54 150 3507
Biso mean--75.54 45.12 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073452
X-RAY DIFFRACTIONf_angle_d0.8254710
X-RAY DIFFRACTIONf_chiral_restr0.047566
X-RAY DIFFRACTIONf_plane_restr0.005604
X-RAY DIFFRACTIONf_dihedral_angle_d13.6762114
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.96-20.36211330.3492276099
2-2.04350.29621490.3121275299
2.0435-2.09110.30281500.2749274499
2.0911-2.14340.27371490.251275099
2.1434-2.20130.2991560.2302271599
2.2013-2.26610.24931440.2167274798
2.2661-2.33920.21661560.2042274698
2.3392-2.42280.2351550.1933271698
2.4228-2.51980.25941720.2051270698
2.5198-2.63450.25831550.1995269796
2.6345-2.77330.24941360.1956270596
2.7733-2.94710.20851300.1939269595
2.9471-3.17450.231210.2005267294
3.1745-3.49380.23131250.1852265393
3.4938-3.99910.1741190.1517263392
3.9991-5.0370.13811290.1302263391
5.037-41.6840.16291570.1578258786

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