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- PDB-7xe3: Crystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024) -

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Basic information

Entry
Database: PDB / ID: 7xe3
TitleCrystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024)
ComponentsLysine-specific histone demethylase 1B
KeywordsOXIDOREDUCTASE / DEMETHYLASE / AMINE OXIDASE / CHROMATIN / HISTONE / FAD / MECHANISM-BASED INHIBITOR
Function / homology
Function and homology information


epigenetic programing of female pronucleus / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / genomic imprinting / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / FAD binding / HDMs demethylate histones / UCH proteinases ...epigenetic programing of female pronucleus / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / genomic imprinting / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / FAD binding / HDMs demethylate histones / UCH proteinases / nucleosome / flavin adenine dinucleotide binding / histone binding / oxidoreductase activity / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / 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
3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal / FLAVIN-ADENINE DINUCLEOTIDE / CITRATE ANION / Lysine-specific histone demethylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsNiwa, H. / Sato, S. / Umehara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K06461, 20H03388, 20K21406 Japan
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2
Authors: Niwa, H. / Watanabe, C. / Sato, S. / Harada, T. / Watanabe, H. / Tabusa, R. / Fukasawa, S. / Shiobara, A. / Hashimoto, T. / Ohno, O. / Nakamura, K. / Tsuganezawa, K. / Tanaka, A. / Shirouzu, ...Authors: Niwa, H. / Watanabe, C. / Sato, S. / Harada, T. / Watanabe, H. / Tabusa, R. / Fukasawa, S. / Shiobara, A. / Hashimoto, T. / Ohno, O. / Nakamura, K. / Tsuganezawa, K. / Tanaka, A. / Shirouzu, M. / Honma, T. / Matsuno, K. / Umehara, T.
History
DepositionMar 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Structure summary / Category: citation / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific histone demethylase 1B
B: Lysine-specific histone demethylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,99816
Polymers178,0292
Non-polymers2,96914
Water3,819212
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A: Lysine-specific histone demethylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6919
Polymers89,0151
Non-polymers1,6768
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific histone demethylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3077
Polymers89,0151
Non-polymers1,2936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.372, 171.226, 201.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
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 , 1 types, 2 molecules AB

#1: Protein Lysine-specific histone demethylase 1B / Flavin-containing amine oxidase domain-containing protein 1 / Lysine-specific histone demethylase 2


Mass: 89014.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1B, AOF1, C6orf193, LSD2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8NB78, [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase

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Non-polymers , 7 types, 226 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-8A2 / 3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal


Mass: 249.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7BrF2O
#5: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 3.48 Å3/Da / Density % sol: 64.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 330mM Ammonium citrate, 26% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.919 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 2.82→48.27 Å / Num. obs: 60041 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 59.05 Å2 / Rsym value: 0.138 / Net I/σ(I): 11.9
Reflection shellResolution: 2.82→2.89 Å / Mean I/σ(I) obs: 1.6 / Rsym value: 1.224

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FWE

4fwe


Resolution: 2.82→48.27 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 23.855
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.222 3004 5.03 %
Rwork0.177 --
obs0.179 60026 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.22 Å2
Refinement stepCycle: LAST / Resolution: 2.82→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11758 0 172 212 12142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712223
X-RAY DIFFRACTIONf_angle_d0.84916577
X-RAY DIFFRACTIONf_dihedral_angle_d13.8614552
X-RAY DIFFRACTIONf_chiral_restr0.0481782
X-RAY DIFFRACTIONf_plane_restr0.0082197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.850.39292100.32583645X-RAY DIFFRACTION100
2.85-2.890.36481910.32253643X-RAY DIFFRACTION100
2.89-2.920.34792190.29183617X-RAY DIFFRACTION100
2.92-2.960.33941840.29163676X-RAY DIFFRACTION100
2.96-30.33242150.28943651X-RAY DIFFRACTION100
3-3.040.2722260.27993636X-RAY DIFFRACTION100
3.04-3.080.31491590.25933710X-RAY DIFFRACTION100
3.08-3.130.33681750.24643664X-RAY DIFFRACTION100
3.13-3.180.29471920.23913659X-RAY DIFFRACTION100
3.18-3.230.26762010.22923664X-RAY DIFFRACTION100
3.23-3.280.25121920.22413667X-RAY DIFFRACTION100
3.28-3.340.24441880.23113693X-RAY DIFFRACTION100
3.34-3.410.32121990.22813614X-RAY DIFFRACTION100
3.41-3.480.27762120.19823629X-RAY DIFFRACTION100
3.48-3.550.21821630.19023676X-RAY DIFFRACTION100
3.55-3.640.20652160.17033648X-RAY DIFFRACTION100
3.64-3.730.18582090.16433627X-RAY DIFFRACTION100
3.73-3.830.21662140.15343655X-RAY DIFFRACTION100
3.83-3.940.19062140.15313677X-RAY DIFFRACTION100
3.94-4.070.19191500.14993731X-RAY DIFFRACTION100
4.07-4.210.18132000.13993610X-RAY DIFFRACTION100
4.21-4.380.1881710.13213678X-RAY DIFFRACTION100
4.38-4.580.16232000.13063675X-RAY DIFFRACTION100
4.58-4.820.18991780.12963662X-RAY DIFFRACTION100
4.82-5.120.17342040.13123637X-RAY DIFFRACTION100
5.12-5.520.19081980.14523672X-RAY DIFFRACTION100
5.52-6.070.21671670.15343690X-RAY DIFFRACTION100
6.07-6.950.18221840.17213684X-RAY DIFFRACTION100
6.95-8.740.17022090.15393654X-RAY DIFFRACTION100
8.75-48.270.22581720.16613681X-RAY DIFFRACTION99
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)
13.3665-0.02360.22923.95970.25833.8594-0.0390.1670.03090.0637-0.00710.88370.1506-0.53730.06130.3983-0.0720.01250.4140.09930.630213.996749.603836.7679
24.40314.04520.70275.07621.4530.6938-0.0293-0.0599-0.38630.24140.1048-0.24250.0752-0.0139-0.07250.44970.04920.01930.29840.07380.41434.313967.433239.9381
31.97490.2313-0.06283.2394-0.00441.1316-0.00530.2218-0.2157-0.28670.1244-0.71860.03590.1502-0.09170.3181-0.00810.07960.3698-0.0870.386851.320694.021734.5731
43.24570.2662-1.03412.5901-0.56064.88820.19470.56390.297-0.41170.1120.549-0.4075-1.5212-0.29310.83090.0771-0.11330.93320.17040.463324.751253.83420.6975
55.1674-2.74841.86445.8281-1.35765.17890.0530.0883-0.2662-0.39680.030.05050.34130.0466-0.08290.5155-0.1037-0.00990.4022-0.0040.253440.990443.207216.0847
62.8244-0.00430.04351.705-0.61822.1026-0.0047-0.0259-0.3912-0.0902-0.1123-0.35890.11060.30370.11390.30430.0306-0.01120.3966-0.01030.619561.895230.113638.9775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 46 THROUGH 233 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 234 THROUGH 404 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 405 THROUGH 822 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 49 THROUGH 214 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 215 THROUGH 377 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 378 THROUGH 822 )

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