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- PDB-5l3d: Human LSD1/CoREST: LSD1 Y761H mutation -

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Basic information

Entry
Database: PDB / ID: 5l3d
TitleHuman LSD1/CoREST: LSD1 Y761H mutation
Components
  • Lysine-specific histone demethylase 1A
  • REST corepressor 1
KeywordsOXIDOREDUCTASE/REPRESSOR / OXIDOREDUCTASE-REPRESSOR complex / Histone demethylase / chromatin / flavin / FAD
Function / homology
Function and homology information


positive regulation of megakaryocyte differentiation / 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 / histone H4K20 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K4 demethylase activity / telomeric repeat-containing RNA binding ...positive regulation of megakaryocyte differentiation / 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 / histone H4K20 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K4 demethylase activity / telomeric repeat-containing RNA binding / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / neuron maturation / muscle cell development / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MRF binding / regulation of androgen receptor signaling pathway / positive regulation of neural precursor cell proliferation / DNA repair complex / 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 / histone deacetylase complex / 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 / transcription repressor complex / epigenetic regulation of gene expression / cellular response to cAMP / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / erythrocyte differentiation / Negative Regulation of CDH1 Gene Transcription / HDACs deacetylate histones / promoter-specific chromatin binding / positive regulation of neuron projection development / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / cerebral cortex development / 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 / chromatin organization / 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 / negative regulation of gene expression / negative regulation of DNA-templated transcription / 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
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1880 / : / Helical region in REST corepressor / : / Histone lysine-specific demethylase / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / ATP synthase, gamma subunit, helix hairpin domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1880 / : / Helical region in REST corepressor / : / Histone lysine-specific demethylase / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / ATP synthase, gamma subunit, helix hairpin domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / : / SANT domain profile. / Amine oxidase / Flavin containing amine oxidoreductase / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Lysine-specific histone demethylase 1A / REST corepressor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsPilotto, S. / Speranzini, V. / Marabelli, C. / Mattevi, A.
CitationJournal: Hum.Mol.Genet. / Year: 2016
Title: LSD1/KDM1A mutations associated to a newly described form of intellectual disability impair demethylase activity and binding to transcription factors.
Authors: Pilotto, S. / Speranzini, V. / Marabelli, C. / Rusconi, F. / Toffolo, E. / Grillo, B. / Battaglioli, E. / Mattevi, A.
History
DepositionApr 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Data collection
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: Lysine-specific histone demethylase 1A
B: REST corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,8743
Polymers146,0882
Non-polymers7861
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-51 kcal/mol
Surface area37910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.309, 177.687, 235.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Lysine-specific histone demethylase 1A / BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2


Mass: 92986.430 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 BL21(DE3) (bacteria) / References: UniProt: O60341, Oxidoreductases
#2: Protein REST corepressor 1 / Protein CoREST


Mass: 53101.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RCOR1, KIAA0071, RCOR / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9UKL0
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 4.3 Å3/Da / Density % sol: 82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: Tartrate 1-1.4 M, ADA 100 mM pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 76680 / % possible obs: 99.2 % / Redundancy: 4.4 % / CC1/2: 0.992 / Rsym value: 0.076 / Net I/σ(I): 10.5
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→100 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / SU B: 9.173 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.168 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21877 1460 1.9 %RANDOM
Rwork0.20759 ---
obs0.20781 75217 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 79.843 Å2
Baniso -1Baniso -2Baniso -3
1-5.45 Å20 Å20 Å2
2---3.07 Å20 Å2
3----2.38 Å2
Refinement stepCycle: 1 / Resolution: 2.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6291 0 53 64 6408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196478
X-RAY DIFFRACTIONr_bond_other_d0.0020.026273
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.978785
X-RAY DIFFRACTIONr_angle_other_deg0.89314426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3735797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90224.475295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.896151130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9631542
X-RAY DIFFRACTIONr_chiral_restr0.0640.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021470
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4457.783194
X-RAY DIFFRACTIONr_mcbond_other3.4427.783193
X-RAY DIFFRACTIONr_mcangle_it5.53911.6713989
X-RAY DIFFRACTIONr_mcangle_other5.53911.6723990
X-RAY DIFFRACTIONr_scbond_it3.4048.1823283
X-RAY DIFFRACTIONr_scbond_other3.4048.1813281
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.72912.0924796
X-RAY DIFFRACTIONr_long_range_B_refined8.1760.9827124
X-RAY DIFFRACTIONr_long_range_B_other8.1860.9827122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 121 -
Rwork0.374 5545 -
obs--99.81 %

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