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- PDB-2uxn: Structural Basis of Histone Demethylation by LSD1 Revealed by Sui... -

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Entry
Database: PDB / ID: 2uxn
TitleStructural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation
Components
  • HISTONE H3.1
  • LYSINE-SPECIFIC HISTONE DEMETHYLASE 1
  • REST COREPRESSOR 1
KeywordsOXIDOREDUCTASE/TRANSCRIPTION REGULATOR / OXIDOREDUCTASE-TRANSCRIPTION REGULATOR COMPLEX / OXIDOREDUCTASE-REPRESSOR COMPLEX / HISTONE DEMETHYLASE / FAD / LSD1 / COREST / REPRESSOR / TRANSCRIPTION REGULATION / HOST-VIRUS INTERACTION / CHROMATIN DEMETHYLATION / NUCLEAR PROTEIN / PHOSPHORYLATION / CHROMATIN REGULATOR / NUCLEOSOMES / TRANSCRIPTION / OXIDOREDUCTASE
Function / homology
Function and homology information


positive regulation of megakaryocyte differentiation / guanine metabolic process / protein demethylation / negative regulation of transcription initiation-coupled chromatin remodeling / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / neuron maturation ...positive regulation of megakaryocyte differentiation / guanine metabolic process / protein demethylation / negative regulation of transcription initiation-coupled chromatin remodeling / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / neuron maturation / muscle cell development / positive regulation of neural precursor cell proliferation / histone H3K9 demethylase activity / MRF binding / regulation of androgen receptor signaling pathway / DNA repair complex / negative regulation of DNA binding / histone demethylase activity / 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 methyltransferase complex / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase complex / positive regulation of cell size / positive regulation of epithelial to mesenchymal transition / Chromatin modifying enzymes / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of protein binding / cellular response to cAMP / positive regulation of protein ubiquitination / transcription repressor complex / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / negative regulation of DNA-binding transcription factor activity / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / epigenetic regulation of gene expression / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / PRC2 methylates histones and DNA / erythrocyte differentiation / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / promoter-specific chromatin binding / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / cellular response to gamma radiation / NoRC negatively regulates rRNA expression / cerebral cortex development / positive regulation of neuron projection development / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / transcription corepressor activity / cellular response to UV / structural constituent of chromatin / p53 binding / nucleosome / flavin adenine dinucleotide binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / regulation of protein localization / HATs acetylate histones / chromatin organization / positive regulation of cold-induced thermogenesis / Senescence-Associated Secretory Phenotype (SASP) / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Oxidative Stress Induced Senescence / transcription regulator complex / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Potential therapeutics for SARS / gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromosome, telomeric region / oxidoreductase activity
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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / FAD/NAD(P)-binding domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Lysine-specific histone demethylase 1A / Histone H3.1 / REST corepressor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.72 Å
AuthorsYang, M. / Culhane, J.C. / Szewczuk, L.M. / Gocke, C.B. / Brautigam, C.A. / Tomchick, D.R. / Machius, M. / Cole, P.A. / Yu, H.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural Basis of Histone Demethylation by Lsd1 Revealed by Suicide Inactivation.
Authors: Yang, M. / Culhane, J.C. / Szewczuk, L.M. / Gocke, C.B. / Brautigam, C.A. / Tomchick, D.R. / Machius, M. / Cole, P.A. / Yu, H.
#1: Journal: Mol.Cell / Year: 2006
Title: Structural Basis for Corest-Dependent Demethylation of Nucleosomes by the Human Lsd1 Histone Demethylase
Authors: Yang, M. / Gocke, C.B. / Luo, X. / Borek, D. / Tomchick, D.R. / Machius, M. / Otwinowski, Z. / Yu, H.
History
DepositionMar 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1
B: REST COREPRESSOR 1
E: HISTONE H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8207
Polymers102,8693
Non-polymers9514
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)119.949, 178.646, 234.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein LYSINE-SPECIFIC HISTONE DEMETHYLASE 1 / FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2 / BRAF35-HDAC COMPLEX PROTEIN BHC110 / ...FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2 / BRAF35-HDAC COMPLEX PROTEIN BHC110 / LYSINE-SPECIFIC DEMETHYLASE 1


Mass: 74126.781 Da / Num. of mol.: 1
Fragment: SWIRM DOMAIN, AMINE OXIDASE DOMAIN AND LINKER, RESIDUES 171-836
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MJ23 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O60341, Oxidoreductases
#2: Protein REST COREPRESSOR 1 / PROTEIN COREST


Mass: 26425.729 Da / Num. of mol.: 1
Fragment: FRAGMENT OF SANT1, LINKER REGION AND SANT2 DOMAIN, RESIDUES 286-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MJ65 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UKL0

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Protein/peptide , 1 types, 1 molecules E

#3: Protein/peptide HISTONE H3.1 / H3/A / H3/B / H3/C / H3/D / H3/F / H3/H / H3/I / H3/J / H3/K / H3/L


Mass: 2316.749 Da / Num. of mol.: 1
Fragment: HISTONE H3-DERIVED SUICIDE INHIBITOR, RESIDUES 2-22
Source method: obtained synthetically
Details: HISTONE H3 N-TERMINAL PEPTIDE (RESIDUES 1-21 ) WITH A PROPARGYL MOIETY AT LYSINE 4 COVALENTLY ATTACHED TO FAD AND SUBSEQUENTLY REDUCED USING SODIUM BOROHYDRIDE
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P68431

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Non-polymers , 4 types, 55 molecules

#4: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT USED CONTAINS A LINKER: (MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFGR) FROM THE CLONING ...THE CONSTRUCT USED CONTAINS A LINKER: (MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFGR) FROM THE CLONING PROCEDURE. LYSINE-4 OF THIS FRAGMENT HAS BEEN MODIFIED BY A MONO- METHYL-N-PROPARGYL GROUP

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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: 6 Å3/Da / Density % sol: 79.6 %
Crystal growpH: 5.6
Details: PROTEIN: 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, AND 5 MM DTT RESERVOIR: 0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, AND 10 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97927
DetectorType: CUSTOM / Detector: CCD / Date: Dec 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.69→48.57 Å / Num. obs: 69440 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 81.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 36.6
Reflection shellResolution: 2.69→2.71 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.8 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.72→49 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.916 / SU B: 19.548 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1502 2.2 %RANDOM
Rwork0.241 ---
obs0.242 66383 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.3 Å20 Å20 Å2
2---3.64 Å20 Å2
3----2.67 Å2
Refinement stepCycle: LAST / Resolution: 2.72→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6337 0 61 51 6449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226550
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.9748887
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.5935805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07324.415299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.083151146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1261544
X-RAY DIFFRACTIONr_chiral_restr0.0810.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025696
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.22925
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24530
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2205
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5081.54133
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87526494
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.92332724
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6684.52392
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.72→2.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.381 86
Rwork0.362 4905
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)
10.26270.4461-0.17870.8959-0.52530.4773-0.0461-0.1213-0.11960.0309-0.2382-0.0454-0.07330.17470.28430.04680.01270.10840.02990.14930.061660.186749.869433.7243
22.4493.1116-1.70224.2012-2.08791.2056-0.32930.35150.2736-0.56350.2371-0.14140.4817-0.03970.0922-0.00010.00020.000100.0001-0.000124.2275-1.597758.3067
32.5369-5.5876-0.093320.09845.94434.2301-0.00370.28580.15590.391-0.3815-0.4790.37590.17150.38520.00020.00050.000300-0.000165.663255.91632.9866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A173 - 836
2X-RAY DIFFRACTION2B308 - 440
3X-RAY DIFFRACTION3E1 - 7

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