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- PDB-5yjb: LSD1-CoREST in complex with 4-[5-(piperidin-4-ylmethoxy)-2-(p-tol... -

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Basic information

Entry
Database: PDB / ID: 5yjb
TitleLSD1-CoREST in complex with 4-[5-(piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile
Components
  • Lysine-specific histone demethylase 1A
  • REST corepressor 1
KeywordsOXIDOREDUCTASE/TRANSCRIPTION/INHIBITOR / DEMETHYLASE / AMINE OXIDASE / CHROMATIN / HISTONE / FAD / COREPRESSOR / OXIDOREDUCTASE-TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of megakaryocyte differentiation / guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / demethylase activity / FAD-dependent H3K4me/H3K4me3 demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development ...positive regulation of megakaryocyte differentiation / guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / demethylase activity / FAD-dependent H3K4me/H3K4me3 demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / neuron maturation / positive regulation of neural precursor cell proliferation / MRF binding / regulation of androgen receptor signaling pathway / DNA repair complex / negative regulation of DNA binding / 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 deacetylase 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 / cellular response to cAMP / transcription repressor complex / negative regulation of protein binding / : / erythrocyte differentiation / positive regulation of protein ubiquitination / Regulation of PTEN gene transcription / epigenetic regulation of gene expression / promoter-specific chromatin binding / HDACs deacetylate histones / negative regulation of DNA-binding transcription factor activity / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / cerebral cortex development / positive regulation of neuron projection development / transcription corepressor activity / cellular response to UV / p53 binding / flavin adenine dinucleotide binding / chromatin organization / positive regulation of cold-induced thermogenesis / regulation of protein localization / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / Estrogen-dependent gene expression / Potential therapeutics for SARS / transcription coactivator activity / chromosome, telomeric region / oxidoreductase activity / 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
Chem-8WC / FLAVIN-ADENINE DINUCLEOTIDE / Lysine-specific histone demethylase 1A / REST corepressor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsNiwa, H. / Sato, S. / Hashimoto, T. / Matsuno, K. / Umehara, T.
CitationJournal: Molecules / Year: 2018
Title: Crystal Structure of LSD1 in Complex with 4-[5-(Piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile.
Authors: Niwa, H. / Sato, S. / Hashimoto, T. / Matsuno, K. / Umehara, T.
History
DepositionOct 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5376
Polymers90,1842
Non-polymers1,3534
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-55 kcal/mol
Surface area37050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.144, 179.624, 234.953
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: 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 KRX (bacteria) / Strain (production host): KRX / 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: Chemical ChemComp-8WC / 4-[2-(4-methylphenyl)-5-(piperidin-4-ylmethoxy)pyridin-3-yl]benzenecarbonitrile


Mass: 383.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25N3O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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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: 7.09 Å3/Da / Density % sol: 82.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M N-(2-ACETAMIDO)IMINODIACETIC ACID (PH 5.5), 1.23M POTASSIUM SODIUM TARTRATE TETRAHYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Apr 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.96→49.16 Å / Num. obs: 53652 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.044 / Rrim(I) all: 0.123 / Net I/σ(I): 16.2
Reflection shellResolution: 2.96→3.05 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.42 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4572 / CC1/2: 0.747 / Rpim(I) all: 0.548 / Rrim(I) all: 1.52 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H6Q

5h6q


Resolution: 2.96→48.82 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 25.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 1053 1.97 %
Rwork0.189 --
obs0.189 53614 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.96→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6219 0 94 0 6313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086446
X-RAY DIFFRACTIONf_angle_d0.9458746
X-RAY DIFFRACTIONf_dihedral_angle_d13.8033892
X-RAY DIFFRACTIONf_chiral_restr0.048976
X-RAY DIFFRACTIONf_plane_restr0.0061150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.02890.38321350.39776660X-RAY DIFFRACTION100
3.0289-3.10460.40821590.35846715X-RAY DIFFRACTION100
3.1046-3.18850.38661110.32246804X-RAY DIFFRACTION100
3.1885-3.28230.31791470.28386701X-RAY DIFFRACTION100
3.2823-3.38820.29321420.23816764X-RAY DIFFRACTION100
3.3882-3.50930.25551290.23856710X-RAY DIFFRACTION100
3.5093-3.64980.22841770.21976705X-RAY DIFFRACTION100
3.6498-3.81580.23211450.2026718X-RAY DIFFRACTION100
3.8158-4.01690.17871270.16866774X-RAY DIFFRACTION100
4.0169-4.26840.14481340.13996714X-RAY DIFFRACTION100
4.2684-4.59780.15791110.12366750X-RAY DIFFRACTION100
4.5978-5.060.18021240.13096742X-RAY DIFFRACTION100
5.06-5.79120.19831250.15946787X-RAY DIFFRACTION100
5.7912-7.29240.21951420.1876746X-RAY DIFFRACTION100
7.2924-48.82830.1821240.16496756X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8195-0.21-0.91091.8655-0.48343.6041-0.095-0.2390.33850.0446-0.0402-0.5134-0.40170.60140.15750.6174-0.1225-0.19160.46610.11940.600915.2127-56.5947-17.0409
22.9016-6.12373.42788.3048-4.83172.6027-0.16480.17650.37990.4356-0.0735-0.468-0.419-0.01310.20491.18120.0296-0.37050.77290.30331.0864-25.8694-14.8152-56.9416
31.7976-0.1138-0.03373.2785-0.12881.7875-0.0720.37380.0944-0.6112-0.2293-0.19330.06670.10650.27810.83220.0127-0.02330.39840.08740.42462.673-62.956-33.7827
43.2026-3.2553.58235.5562-4.63196.52510.27550.242-0.1745-0.0577-0.08170.28450.1349-0.3797-0.19340.76680.0112-0.1830.62250.17770.7601-26.4831-26.6262-56.2624
54.70281.5054-0.69110.589-0.74942.70170.3717-1.23010.32060.6382-0.0266-0.8279-0.63560.7918-0.33371.3505-0.1726-0.26291.11350.00531.6335-33.598226.2815-66.3882
67.1637-2.2213-4.11131.9274-0.04044.7672-0.398-2.2212-0.66640.71640.3075-0.91290.25170.34210.05371.73150.0259-0.54691.05550.19540.8831-44.018223.3215-61.819
76.80391.02585.38724.07370.28179.70840.2042-1.469-0.03292.4537-0.2242-0.3171-0.1502-0.06130.04141.84030.1702-0.26061.2486-0.03820.759-50.416825.6474-54.7992
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 172 THROUGH 371 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 372 THROUGH 513 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 514 THROUGH 832 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 309 THROUGH 370 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 371 THROUGH 384 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 385 THROUGH 413 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 414 THROUGH 439 )

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