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- PDB-7jjm: Crystal structure of Importin alpha 2 in complex with LSD1 NLS -

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Basic information

Entry
Database: PDB / ID: 7jjm
TitleCrystal structure of Importin alpha 2 in complex with LSD1 NLS
Components
  • Importin subunit alpha-1
  • Lysine-specific histone demethylase 1A
KeywordsPROTEIN TRANSPORT / Importin Demethylase
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 / regulation of double-strand break repair via homologous recombination / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 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 / positive regulation of neuron projection development / HDMs demethylate histones / cerebral cortex development / protein modification process / protein import into nucleus / cytoplasmic stress granule / 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 / DNA-binding transcription factor binding / Estrogen-dependent gene expression / 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: 2.06 Å
AuthorsTu, W.J. / McGuaig, R. / Tan, H.Y.A. / Hardy, C. / Seddiki, N. / Ali, S. / Dahlstrom, J.E. / Bean, E.G. / Dunn, J. / Forwood, J.K. ...Tu, W.J. / McGuaig, R. / Tan, H.Y.A. / Hardy, C. / Seddiki, N. / Ali, S. / Dahlstrom, 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.
Citation
Journal: 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.
#1: Journal: 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)54,1513
Polymers54,1152
Non-polymers351
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-8 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.610, 90.050, 99.750
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: 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
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.26 Å3/Da / Density % sol: 62.29 %
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: 2.06→41.04 Å / Num. obs: 43845 / % possible obs: 98.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 36.59 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.159 / Net I/σ(I): 4.3
Reflection shellResolution: 2.06→2.06 Å / Rmerge(I) obs: 0.759 / Num. unique obs: 2917 / CC1/2: 0.675

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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: 2.06→41.038 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 2183 4.99 %
Rwork0.2199 41608 -
obs0.2218 43791 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.35 Å2 / Biso mean: 50.7747 Å2 / Biso min: 20.74 Å2
Refinement stepCycle: final / Resolution: 2.06→41.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 1 103 3370
Biso mean--60.91 42.73 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023360
X-RAY DIFFRACTIONf_angle_d0.5024586
X-RAY DIFFRACTIONf_chiral_restr0.037554
X-RAY DIFFRACTIONf_plane_restr0.003587
X-RAY DIFFRACTIONf_dihedral_angle_d11.6462066
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.06-2.10480.35761300.3061229389
2.1048-2.15380.32521620.27682570100
2.1538-2.20760.28711310.25962609100
2.2076-2.26730.26331460.2395257599
2.2673-2.3340.25591470.2322582100
2.334-2.40930.23961350.23742607100
2.4093-2.49540.27191440.2342625100
2.4954-2.59530.29141300.23542615100
2.5953-2.71340.28361330.2478261099
2.7134-2.85650.23691230.22842629100
2.8565-3.03540.25831390.2452638100
3.0354-3.26970.28731240.2462656100
3.2697-3.59850.30111400.2334262699
3.5985-4.11880.23841440.2008264799
4.1188-5.18760.23981440.1818265799
5.1876-41.0380.21151110.1894266994

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