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- PDB-5x60: Crystal structure of LSD1-CoREST in complex with peptide 9 -

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Basic information

Entry
Database: PDB / ID: 5x60
TitleCrystal structure of LSD1-CoREST in complex with peptide 9
Components
  • Lysine-specific histone demethylase 1A
  • PEPTIDE SRTMQTARKSTGGKAPRKQL
  • REST corepressor 1
KeywordsOXIDOREDUCTASE/TRANSCRIPTION / DEMETHYLASE / AMINE OXIDASE / CHROMATIN / HISTONE / FAD / COREPRESSOR / OXIDOREDUCTASE-TRANSCRIPTION complex
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 / Chromatin modifying enzymes / transcription repressor complex / telomere organization / Interleukin-7 signaling / epigenetic regulation of gene expression / RNA Polymerase I Promoter Opening / cellular response to cAMP / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / erythrocyte differentiation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Negative Regulation of CDH1 Gene Transcription / HDACs deacetylate histones / promoter-specific chromatin binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / positive regulation of neuron projection development / Formation of the beta-catenin:TCF transactivating complex / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cerebral cortex development / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / RMTs methylate histone arginines / HCMV Early Events / p53 binding / structural constituent of chromatin / cellular response to UV / transcription corepressor activity / flavin adenine dinucleotide binding / nucleosome / nucleosome assembly / regulation of protein localization / positive regulation of cold-induced thermogenesis / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / 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
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 / Histone H3 signature 1. / FAD/NAD(P)-binding domain superfamily / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / 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 / REST corepressor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsKikuchi, M. / Amano, Y. / Sato, S. / Yokoyama, S. / Umezawa, N. / Higuchi, T. / Umehara, T.
CitationJournal: Bioorg. Med. Chem. / Year: 2017
Title: Development and crystallographic evaluation of histone H3 peptide with N-terminal serine substitution as a potent inhibitor of lysine-specific demethylase 1.
Authors: Amano, Y. / Kikuchi, M. / Sato, S. / Yokoyama, S. / Umehara, T. / Umezawa, N. / Higuchi, T.
History
DepositionFeb 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific histone demethylase 1A
B: REST corepressor 1
C: PEPTIDE SRTMQTARKSTGGKAPRKQL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4547
Polymers92,3933
Non-polymers1,0624
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9650 Å2
ΔGint-57 kcal/mol
Surface area36890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.005, 180.359, 233.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 74333.039 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 172-833
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: O60341, Oxidoreductases
#2: Protein REST corepressor 1 / Protein CoREST


Mass: 15850.929 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 311-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RCOR1, KIAA0071, RCOR / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q9UKL0

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide PEPTIDE SRTMQTARKSTGGKAPRKQL


Mass: 2208.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS

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Non-polymers , 3 types, 64 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 6.94 Å3/Da / Density % sol: 82.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M N-(2-acetamido)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 71152 / % possible obs: 99.4 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.9
Reflection shellResolution: 2.68→2.73 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3551 / CC1/2: 0.887 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V1D

2v1d


Resolution: 2.69→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.345 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23626 1376 1.9 %RANDOM
Rwork0.2214 ---
obs0.22169 69775 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 75.272 Å2
Baniso -1Baniso -2Baniso -3
1-7.75 Å2-0 Å20 Å2
2---5.68 Å2-0 Å2
3----2.07 Å2
Refinement stepCycle: 1 / Resolution: 2.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6329 0 71 60 6460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196566
X-RAY DIFFRACTIONr_bond_other_d0.0020.026337
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.9718907
X-RAY DIFFRACTIONr_angle_other_deg0.842314569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9635814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85124.564298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.821151134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0721542
X-RAY DIFFRACTIONr_chiral_restr0.0550.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217428
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021489
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_it2.3327.4533250
X-RAY DIFFRACTIONr_mcbond_other2.3297.4523249
X-RAY DIFFRACTIONr_mcangle_it3.98311.1744063
X-RAY DIFFRACTIONr_mcangle_other3.98311.1754064
X-RAY DIFFRACTIONr_scbond_it2.1867.6973316
X-RAY DIFFRACTIONr_scbond_other2.1867.6973316
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.88611.4194844
X-RAY DIFFRACTIONr_long_range_B_refined6.13385.9657211
X-RAY DIFFRACTIONr_long_range_B_other6.12685.9747204
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.688→2.758 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 87 -
Rwork0.354 5089 -
obs--98.84 %

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