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- PDB-7xe2: Crystal structure of LSD2 in complex with trans-4-Br-PCPA -

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Entry
Database: PDB / ID: 7xe2
TitleCrystal structure of LSD2 in complex with trans-4-Br-PCPA
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 / genomic imprinting / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / FAD binding / transcription initiation-coupled chromatin remodeling / HDMs demethylate histones / UCH proteinases ...epigenetic programing of female pronucleus / genomic imprinting / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / FAD binding / transcription initiation-coupled chromatin remodeling / HDMs demethylate histones / UCH proteinases / nucleosome / flavin adenine dinucleotide binding / histone binding / oxidoreductase activity / chromatin remodeling / chromatin binding / chromatin / 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 ...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-bromophenyl)propanal / FLAVIN-ADENINE DINUCLEOTIDE / CITRATE ANION / TRIETHYLENE GLYCOL / Lysine-specific histone demethylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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:
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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)183,21623
Polymers178,0292
Non-polymers5,18721
Water17,457969
1
A: Lysine-specific histone demethylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,91614
Polymers89,0151
Non-polymers2,90113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific histone demethylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3009
Polymers89,0151
Non-polymers2,2868
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.582, 170.082, 201.107
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
Components on special symmetry positions
IDModelComponents
11A-1452-

HOH

21A-1466-

HOH

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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, 990 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


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-DIJ / 3-(4-bromophenyl)propanal


Mass: 213.071 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H9BrO
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / 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: 3.45 Å3/Da / Density % sol: 64.33 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / Details: 300mM Ammonium citrate, 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9195 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 2.05→48.16 Å / Num. obs: 152020 / % possible obs: 99.7 % / Redundancy: 11.3 % / Biso Wilson estimate: 33.44 Å2 / Rsym value: 0.081 / Net I/σ(I): 22.6
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 10 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.965 / % possible all: 93.2

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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: 2.05→46.56 Å / SU ML: 0.218 / Cross valid method: FREE R-VALUE / σ(F): 1.13 / Phase error: 21.426
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.194 7595 5.01 %
Rwork0.167 --
obs0.168 151961 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.77 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11801 0 315 969 13085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812467
X-RAY DIFFRACTIONf_angle_d0.86316936
X-RAY DIFFRACTIONf_dihedral_angle_d13.0224720
X-RAY DIFFRACTIONf_chiral_restr0.0541815
X-RAY DIFFRACTIONf_plane_restr0.0092291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.34994500.32148193X-RAY DIFFRACTION88
2.08-2.10.31114590.27379482X-RAY DIFFRACTION100
2.1-2.130.27574690.25929357X-RAY DIFFRACTION100
2.13-2.150.27565280.24299339X-RAY DIFFRACTION100
2.15-2.180.24834970.22649471X-RAY DIFFRACTION100
2.18-2.210.25774740.21879458X-RAY DIFFRACTION100
2.21-2.240.24265420.21619287X-RAY DIFFRACTION100
2.24-2.280.25434710.21269471X-RAY DIFFRACTION100
2.28-2.310.23054650.20879390X-RAY DIFFRACTION100
2.31-2.350.22785180.20479396X-RAY DIFFRACTION100
2.35-2.390.25164990.20199379X-RAY DIFFRACTION100
2.39-2.430.24664820.20169402X-RAY DIFFRACTION100
2.43-2.480.22555010.19079382X-RAY DIFFRACTION100
2.48-2.530.2264950.18399457X-RAY DIFFRACTION100
2.53-2.590.22845250.17979404X-RAY DIFFRACTION100
2.59-2.650.21234960.17889327X-RAY DIFFRACTION100
2.65-2.710.21865080.17429459X-RAY DIFFRACTION100
2.71-2.790.21794700.17739388X-RAY DIFFRACTION100
2.79-2.870.23984720.18319447X-RAY DIFFRACTION100
2.87-2.960.2345450.18859296X-RAY DIFFRACTION100
2.96-3.070.21735090.18349456X-RAY DIFFRACTION100
3.07-3.190.19484780.17059439X-RAY DIFFRACTION100
3.19-3.340.184880.16629433X-RAY DIFFRACTION100
3.34-3.510.18154970.15799349X-RAY DIFFRACTION100
3.51-3.730.16155450.14759356X-RAY DIFFRACTION100
3.73-4.020.1675020.1339357X-RAY DIFFRACTION100
4.02-4.420.14554590.12449480X-RAY DIFFRACTION100
4.42-5.060.14195010.12219394X-RAY DIFFRACTION100
5.06-6.380.16184840.14289398X-RAY DIFFRACTION100
6.38-46.560.15844700.159397X-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)
12.1638-0.30750.36662.4383-0.05962.8229-0.07730.1268-0.14810.0602-0.03720.84380.2064-0.57620.08960.2465-0.09770.04540.36440.02590.623911.467147.145937.877
21.47732.25570.27493.50480.70840.3823-0.02760.0115-0.021-0.00960.07740.22490.0139-0.0747-0.05890.20490.01590.020.23550.05370.252331.062564.862538.1349
31.1207-0.1068-0.07072.0916-0.060.50250.02260.12460.0511-0.24450.0496-0.1858-0.02240.0229-0.06110.1999-0.01130.06580.2298-0.0030.182851.53593.486234.4143
41.09830.215-0.44591.757-0.66772.9906-0.00350.20120.1957-0.4190.20790.346-0.1923-0.9726-0.16920.48610.0171-0.1390.59990.07190.354326.314349.98554.8081
53.9062-1.12812.50361.5182-0.65721.90830.15550.5576-0.029-0.3764-0.0152-0.19560.1180.2803-0.13530.3789-0.03580.02920.3391-0.02140.196948.227544.126414.9789
61.4639-0.1340.00251.5081-0.43381.08890.0484-0.1381-0.3748-0.02420.04770.06690.1640.0366-0.09440.21480.0039-0.0710.3246-0.02450.52161.764929.159440.767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 47 THROUGH 190 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 191 THROUGH 404 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 405 THROUGH 822 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 49 THROUGH 277 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 278 THROUGH 404 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 405 THROUGH 822 )

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