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- PDB-2x0l: Crystal structure of a neuro-specific splicing variant of human h... -

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Basic information

Entry
Database: PDB / ID: 2x0l
TitleCrystal structure of a neuro-specific splicing variant of human histone lysine demethylase LSD1.
Components
  • HISTONE H3 PEPTIDE
  • LYSINE-SPECIFIC HISTONE DEMETHYLASE 1
  • REST COREPRESSOR 1RCOR1
KeywordsTRANSCRIPTION / REPRESSOR COMPLEX / CHROMATIN REMODELLING / AMINE OXIDASE / HOST-VIRUS INTERACTION / TRANSCRIPTION REGULATION / PHOSPHOPROTEIN / OXIDOREDUCTASE / NUCLEAR PROTEIN / CHROMATIN REGULATOR / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


positive regulation of megakaryocyte differentiation / guanine metabolic process / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / protein demethylation / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / muscle cell development / histone H3K4 demethylase activity ...positive regulation of megakaryocyte differentiation / guanine metabolic process / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / protein demethylation / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / muscle cell development / histone H3K4 demethylase activity / positive regulation of neural precursor cell proliferation / neuron maturation / MRF binding / regulation of androgen receptor signaling pathway / DNA repair complex / DNA repair-dependent chromatin remodeling / nuclear androgen receptor binding / regulation of double-strand break repair via homologous recombination / positive regulation of neuroblast proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of stem cell proliferation / negative regulation of DNA binding / histone H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase complex / positive regulation of cell size / histone demethylase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to fungicide / cellular response to cAMP / transcription repressor complex / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / erythrocyte differentiation / DNA methylation / Condensation of Prophase Chromosomes / nuclear receptor coactivator activity / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / negative regulation of protein binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / Defective pyroptosis / promoter-specific chromatin binding / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / cellular response to gamma radiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / positive regulation of neuron projection development / cerebral cortex development / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / transcription corepressor activity / cellular response to UV / regulation of protein localization / nucleosome / p53 binding / flavin adenine dinucleotide binding / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cold-induced thermogenesis / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / chromosome, telomeric region / transcription coactivator activity / oxidoreductase activity / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1880 / : / Helical region in REST corepressor / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Histone lysine-specific demethylase / SWIRM domain / SWIRM domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1880 / : / Helical region in REST corepressor / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Histone lysine-specific demethylase / SWIRM domain / SWIRM domain / SWIRM domain profile. / ATP synthase, gamma subunit, helix hairpin domain / SANT domain profile. / SANT domain / Amine oxidase / Flavin containing amine oxidoreductase / 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 / Histone H3 signature 1. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / FAD/NAD(P)-binding domain superfamily / Histone-fold / 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 / Histone H3.1 / Histone H3-7 / REST corepressor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZibetti, C. / Adamo, A. / Binda, C. / Forneris, F. / Verpelli, C. / Ginelli, E. / Mattevi, A. / Sala, C. / Battaglioli, E.
CitationJournal: J.Neurosci. / Year: 2010
Title: Alternative Splicing of the Histone Demethylase Lsd1/Kdm1 Contributes to the Modulation of Neurite Morphogenesis in the Mammalian Nervous System.
Authors: Zibetti, C. / Adamo, A. / Binda, C. / Forneris, F. / Toffolo, E. / Verpelli, C. / Ginelli, E. / Mattevi, A. / Sala, C. / Battaglioli, E.
History
DepositionDec 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references / Refinement description ...Database references / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1
B: REST COREPRESSOR 1
C: HISTONE H3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4924
Polymers98,7063
Non-polymers7861
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-55.7 kcal/mol
Surface area38130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.690, 181.210, 233.450
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 1 / FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2 / BRAF35-HDAC COMPLEX PROTEIN BHC110


Mass: 81723.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60341, Oxidoreductases
#2: Protein REST COREPRESSOR 1 / RCOR1 / PROTEIN COREST / COREPRESSOR COREST


Mass: 15317.435 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9UKL0
#3: Protein/peptide HISTONE H3 PEPTIDE


Mass: 1664.928 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-17 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q5TEC6, UniProt: P68431*PLUS
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
Sequence detailsSPLICING VARIANT FORM OF THE PROTEIN LSD1: BETWEEN RESIDUE 369 AND 370 OF CHAIN A THERE ARE 4 ...SPLICING VARIANT FORM OF THE PROTEIN LSD1: BETWEEN RESIDUE 369 AND 370 OF CHAIN A THERE ARE 4 ADDITIONAL (DTVK) RESIDUES THAT HAVE BEEN MARKED AS 369A, 369B, 369C, 369D.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.7 Å3/Da / Density % sol: 78 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→70 Å / Num. obs: 49397 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.2

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Processing

Software
NameVersionClassification
REFMAC5.4.0078refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IW5

2iw5


Resolution: 3→71.5 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.868 / SU B: 11.819 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25195 960 1.9 %RANDOM
Rwork0.21207 ---
obs0.21288 49397 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.132 Å2
Baniso -1Baniso -2Baniso -3
1-4.37 Å20 Å20 Å2
2---3.03 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 3→71.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6438 0 53 0 6491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226625
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9738984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8955816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4524.415299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.296151160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3611544
X-RAY DIFFRACTIONr_chiral_restr0.1030.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214973
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7271.54082
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39626593
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.71632543
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0794.52391
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 67 -
Rwork0.313 3635 -
obs--99.65 %

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