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- PDB-7jjl: Crystal structure of Importin Alpha 3 in complex with human LSD1 NLS -

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Basic information

Entry
Database: PDB / ID: 7jjl
TitleCrystal structure of Importin Alpha 3 in complex with human LSD1 NLS
Components
  • Importin subunit alpha-3
  • Lysine-specific histone demethylase 1A
KeywordsPROTEIN TRANSPORT / demethylase Importin alpha
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 / dopamine secretion / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex ...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 / dopamine secretion / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / neuron maturation / muscle cell development / nuclear localization sequence binding / 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 / nuclear pore / 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 / male germ cell nucleus / HDACs deacetylate histones / promoter-specific chromatin binding / response to hydrogen peroxide / 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 / ISG15 antiviral mechanism / protein import into nucleus / p53 binding / cellular response to UV / transcription corepressor activity / flavin adenine dinucleotide binding / regulation of protein localization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / nuclear membrane / transcription regulator complex / gene expression / 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 / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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 / cytoplasm
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
Importin subunit alpha-3 / Lysine-specific histone demethylase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTu, W.J. / McCuaig, R. / Tan, H.Y.A. / Hardy, K. / Seddiki, N. / Ali, S. / Dahlstrom, J.E. / Bean, E.G. / Dunn, J. / Forwood, J.K. ...Tu, W.J. / McCuaig, R. / Tan, H.Y.A. / Hardy, K. / Seddiki, N. / Ali, S. / Dahlstrom, J.E. / Bean, E.G. / Dunn, J. / Forwood, J.K. / Tsimbalyuk, S. / Smith, K. / 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: Importin subunit alpha-3
B: Lysine-specific histone demethylase 1A


Theoretical massNumber of molelcules
Total (without water)54,2652
Polymers54,2652
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint0 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.920, 89.120, 143.530
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-3 / Importin alpha Q1 / Qip1 / Karyopherin subunit alpha-4


Mass: 51120.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA4, QIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00629
#2: 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: 3144.527 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.82 Å3/Da / Density % sol: 56.44 %
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: 2.6→33.31 Å / Num. obs: 19536 / % possible obs: 99.5 % / Redundancy: 3.7 % / CC1/2: 0.997 / Net I/σ(I): 2.1
Reflection shellResolution: 2.6→2.6 Å / Rmerge(I) obs: 0.493 / Num. unique obs: 2323 / CC1/2: 0.778

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIXv1.12refinement
PDB_EXTRACT3.25data extraction
Aimlessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BVZ

6bvz


Resolution: 2.6→33.31 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.919 / SU B: 0.009 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 1024 5.3 %RANDOM
Rwork0.2039 ---
obs0.2071 18464 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 185.69 Å2 / Biso mean: 66.286 Å2 / Biso min: 29.89 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.6→33.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 0 1 3231
Biso mean---46.42 -
Num. residues----418
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 67 -
Rwork0.335 1362 -
all-1429 -
obs--99.51 %

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