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- PDB-8inl: LSD1 in complex with S2172 -

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Basic information

Entry
Database: PDB / ID: 8inl
TitleLSD1 in complex with S2172
ComponentsLysine-specific histone demethylase 1A
KeywordsOXIDOREDUCTASE/INHIBITOR / DEMETHYLASE / AMINE OXIDASE / CHROMATIN / HISTONE / FAD / MECHANISM-BASED INHIBITOR / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


guanine metabolic process / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / telomeric repeat-containing RNA binding / demethylase activity / regulation of DNA methylation-dependent heterochromatin formation / histone H3K4 demethylase activity / muscle cell development / positive regulation of neural precursor cell proliferation ...guanine metabolic process / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / telomeric repeat-containing RNA binding / demethylase activity / regulation of DNA methylation-dependent heterochromatin formation / histone H3K4 demethylase activity / muscle cell development / positive regulation of neural precursor cell proliferation / neuron maturation / regulation of androgen receptor signaling pathway / MRF binding / 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 / positive regulation of cell size / histone demethylase activity / response to fungicide / cellular response to cAMP / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / nuclear receptor coactivator activity / negative regulation of protein binding / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / 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 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / cerebral cortex development / positive regulation of neuron projection development / cellular response to UV / regulation of protein localization / p53 binding / flavin adenine dinucleotide binding / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / 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 / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Histone lysine-specific demethylase / SWIRM domain / SWIRM domain / SWIRM domain profile. / Amine oxidase / Flavin containing amine oxidoreductase / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-DJ0 / FLAVIN-ADENINE DINUCLEOTIDE / L(+)-TARTARIC ACID / Lysine-specific histone demethylase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsNiwa, H. / Sato, S. / Umehara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: LSD1 in complex with S2172
Authors: Niwa, H. / Sato, S. / Umehara, T.
History
DepositionMar 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0059
Polymers74,3331
Non-polymers1,6728
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.101, 187.101, 106.945
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

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Protein , 1 types, 1 molecules A

#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
Source: (gene. exp.) Homo sapiens (human) / Gene: LSD1 / Plasmid: PETDUET-1 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)
References: UniProt: O60341, [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase

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Non-polymers , 5 types, 65 molecules

#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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: obtained synthetically / Formula: C16H14F2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.63 Å3/Da / Density % sol: 66.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES (pH 6.5), 0.2M diammonium tartrate, 0.0005M TCEP, 14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→48.21 Å / Num. obs: 33642 / % possible obs: 100 % / Redundancy: 40.9 % / Biso Wilson estimate: 73.3 Å2 / CC1/2: 1 / Rpim(I) all: 0.021 / Rrim(I) all: 0.138 / Rsym value: 0.136 / Net I/σ(I): 22.3
Reflection shellResolution: 2.62→2.74 Å / Redundancy: 42.8 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4040 / CC1/2: 0.798 / Rpim(I) all: 0.574 / Rrim(I) all: 3.769 / Rsym value: 3.725 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→48.21 Å / SU ML: 0.399 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 28.149
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2159 1702 5.03 %
Rwork0.1796 59785 -
obs0.1816 33600 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.91 Å2
Refinement stepCycle: LAST / Resolution: 2.62→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5081 0 113 57 5251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00655301
X-RAY DIFFRACTIONf_angle_d0.8017186
X-RAY DIFFRACTIONf_chiral_restr0.0448800
X-RAY DIFFRACTIONf_plane_restr0.0066967
X-RAY DIFFRACTIONf_dihedral_angle_d13.76761998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.660.46821600.37382597X-RAY DIFFRACTION99.82
2.66-2.70.36341210.33042575X-RAY DIFFRACTION99.96
2.7-2.740.28661060.3052658X-RAY DIFFRACTION99.96
2.74-2.790.33171070.27762623X-RAY DIFFRACTION100
2.79-2.840.31361340.26672616X-RAY DIFFRACTION99.96
2.84-2.90.30651290.24772599X-RAY DIFFRACTION99.96
2.9-2.960.31781200.25212613X-RAY DIFFRACTION100
2.96-3.020.27481260.2612618X-RAY DIFFRACTION99.96
3.02-3.090.34241410.27162579X-RAY DIFFRACTION100
3.09-3.170.27421610.23882592X-RAY DIFFRACTION100
3.17-3.250.30281600.22632563X-RAY DIFFRACTION100
3.25-3.350.26421420.21152608X-RAY DIFFRACTION100
3.35-3.460.25651220.19092608X-RAY DIFFRACTION99.89
3.46-3.580.21351370.19742576X-RAY DIFFRACTION100
3.58-3.720.25111480.20532601X-RAY DIFFRACTION100
3.73-3.890.24441370.17352614X-RAY DIFFRACTION100
3.89-4.10.21651380.16252581X-RAY DIFFRACTION100
4.1-4.360.18641760.14722572X-RAY DIFFRACTION100
4.36-4.690.18091450.13972598X-RAY DIFFRACTION100
4.69-5.160.17331670.14392575X-RAY DIFFRACTION100
5.16-5.910.19121490.16182581X-RAY DIFFRACTION100
5.91-7.440.20931360.16612605X-RAY DIFFRACTION100
7.44-48.210.11871070.13562633X-RAY DIFFRACTION99.64
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)
12.06459749087-1.19126629291-0.2227551687292.649402293930.4424370715681.252589033190.04702197443410.187424813958-0.01401114468420.2965199171660.0588235986884-0.2620167172730.1256079294690.322213813726-0.1082191600090.656183656376-0.1479563722840.07462406793710.652251070991-0.1648892415870.5124021968444.675679416538.1053504924-21.7270693431
20.5766783821.016022383711.021848616814.228577535275.233305983656.60129550052-0.2064272680450.08170463619380.134652462568-0.1845827315010.465824335207-0.219754492535-0.8018937878130.756633033024-0.2212229904351.10709662268-0.1894072469460.07077647164870.884972533646-0.1855171927640.72136989541436.014878894382.436953793929.5184379664
31.37675527319-0.2128622991460.141503886732.252549496520.6650711840362.091336808940.0827795540181-0.1225196384870.0009401085894570.28222704825-0.05412258903490.156209939418-0.00311215222491-0.128288320056-0.02872450014760.572127309052-0.1736419021110.1632124680970.565354125751-0.1172464496290.49868196747325.748577881647.3112023694-14.1363439142
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 171 through 371 )171 - 3711 - 201
22chain 'A' and (resid 372 through 513 )372 - 513202 - 336
33chain 'A' and (resid 514 through 832 )514 - 832337 - 648

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