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- PDB-6kgm: LSD1-CoREST-S2116 five-membered ring adduct model -

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Basic information

Entry
Database: PDB / ID: 6kgm
TitleLSD1-CoREST-S2116 five-membered ring adduct model
Components
  • Lysine-specific histone demethylase 1A
  • REST corepressor 1
KeywordsOXIDOREDUCTASE / DEMETHYLASE / AMINE OXIDASE / CHROMATIN / HISTONE / FAD / MECHANISM-BASED INHIBITOR
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 / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / neuron maturation / muscle cell development ...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 / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / neuron maturation / muscle cell development / 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 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 / 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 / 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 / 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
Chem-DJ0 / 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: 2.62 Å
AuthorsNiwa, H. / Sato, S. / Umehara, T.
CitationJournal: Chemmedchem / Year: 2020
Title: Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors.
Authors: Niwa, H. / Sato, S. / Handa, N. / Sengoku, T. / Umehara, T. / Yokoyama, S.
History
DepositionJul 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 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)91,7069
Polymers90,1842
Non-polymers1,5227
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-48 kcal/mol
Surface area37000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.451, 178.696, 235.256
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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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
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / 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
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Homo sapiens (human) / Gene: RCOR1, KIAA0071, RCOR / Production host: Escherichia coli KRX (bacteria) / Strain (production host): KRX / References: UniProt: Q9UKL0

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Non-polymers , 4 types, 61 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DJ0 / 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal


Mass: 276.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H14F2O2
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Nonpolymer details6KGM and 6KGN use the same data but have ligand models with possible different configurations.

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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: 7.02 Å3/Da / Density % sol: 82.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.28 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→49.13 Å / Num. obs: 76266 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 68.02 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.033 / Rrim(I) all: 0.091 / Rsym value: 0.085 / Net I/σ(I): 15.7
Reflection shellResolution: 2.62→2.67 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4451 / CC1/2: 0.734 / Rpim(I) all: 0.562 / Rrim(I) all: 1.563 / Rsym value: 1.458 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→49.13 Å / SU ML: 0.3637 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 23.1998
RfactorNum. reflection% reflection
Rfree0.1947 2866 1.95 %
Rwork0.1755 --
obs0.1759 76234 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 90.42 Å2
Refinement stepCycle: LAST / Resolution: 2.62→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6239 0 103 54 6396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00766472
X-RAY DIFFRACTIONf_angle_d0.9048777
X-RAY DIFFRACTIONf_chiral_restr0.0541978
X-RAY DIFFRACTIONf_plane_restr0.00621174
X-RAY DIFFRACTIONf_dihedral_angle_d12.78273943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.670.36471540.3817133X-RAY DIFFRACTION99.52
2.67-2.710.28231210.34717220X-RAY DIFFRACTION99.74
2.71-2.770.32581270.31817238X-RAY DIFFRACTION99.7
2.77-2.820.31851480.29277164X-RAY DIFFRACTION99.82
2.82-2.880.31561350.27917292X-RAY DIFFRACTION99.89
2.88-2.950.27331520.25187209X-RAY DIFFRACTION99.92
2.95-3.020.25721460.24537199X-RAY DIFFRACTION99.86
3.02-3.110.24781710.23187192X-RAY DIFFRACTION99.92
3.11-3.20.18221300.22387237X-RAY DIFFRACTION99.96
3.2-3.30.21021310.19277196X-RAY DIFFRACTION99.97
3.3-3.420.2141600.18667244X-RAY DIFFRACTION99.91
3.42-3.560.21281580.17997244X-RAY DIFFRACTION99.95
3.56-3.720.21431720.17577174X-RAY DIFFRACTION99.97
3.72-3.910.1661550.15867188X-RAY DIFFRACTION99.97
3.91-4.160.14771510.13727261X-RAY DIFFRACTION99.96
4.16-4.480.14861160.1277232X-RAY DIFFRACTION100
4.48-4.930.18891220.12427214X-RAY DIFFRACTION99.97
4.93-5.640.16891380.14867266X-RAY DIFFRACTION100
5.64-7.110.16531470.17527225X-RAY DIFFRACTION99.97
7.11-49.130.17521320.15597215X-RAY DIFFRACTION99.42
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)
11.786855343670.0078681215084-0.7981930863211.75657404393-0.2832147267993.48360378171-0.0780276405991-0.3192578689130.2335268508130.192469858349-0.157959779797-0.571245297692-0.3941059556360.802030944820.2088590357750.574624023083-0.0968709769334-0.2141820426270.649309981910.1710552982950.70424832927315.3617535376-56.2372424513-16.8054886021
22.33135861744-5.524072087772.908916945987.37511682672-4.255360465012.07220488429-0.02578079504810.1930686441320.2628354592730.291131636954-0.136436170665-0.19616572648-0.3232785301050.08912112093910.1721393181151.046923976140.0469784222143-0.3387897110450.7800337254750.3144854470091.23141697437-25.741308354-14.5510178439-57.0451314671
31.868648391630.0289762565218-0.257781325913.23702678143-0.8886079300672.49863861182-0.1105200968370.3098616843510.0752248448683-0.378738817779-0.218993711814-0.1623635507180.09965058483430.1673052709590.31836522080.5939545641580.0221565560233-0.04009128232850.4395815088760.05626529687810.4709217406222.79903848159-62.4796431363-33.5931336323
43.28984082418-4.471341306713.854564301646.38484459672-5.078867940034.210862700880.3532431414780.202530807843-0.0198506420537-0.267384533246-0.04394983933360.3676905113710.121244047006-0.239200114193-0.3165975813770.8892109965260.0536160580084-0.1889971437050.837045829830.2235427851251.09041703812-26.3090775579-26.3850367439-56.5376387502
56.18708776209-2.0396227475-1.421762793056.924007397482.423200503153.90410191302-0.288919233332-1.703370545510.2037332897271.689137060320.131486439173-1.024006414040.03844713261440.2293176550580.1316339600631.32056818815-0.0401521851314-0.4525174824541.008660893630.08593009567940.791737245876-44.428727407425.0780443288-60.2127101362
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 439 )

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