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- PDB-2iw5: Structural Basis for CoREST-Dependent Demethylation of Nucleosome... -

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Basic information

Entry
Database: PDB / ID: 2iw5
TitleStructural Basis for CoREST-Dependent Demethylation of Nucleosomes by the Human LSD1 Histone Demethylase
Components
  • LYSINE-SPECIFIC HISTONE DEMETHYLASE 1
  • REST COREPRESSOR 1RCOR1
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 / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / protein demethylation / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / muscle cell development / histone H3K4 demethylase activity ...positive regulation of megakaryocyte differentiation / guanine metabolic process / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / protein demethylation / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / telomeric repeat-containing RNA binding / regulation of DNA methylation-dependent heterochromatin formation / muscle cell development / histone H3K4 demethylase activity / positive regulation of neural precursor cell proliferation / neuron maturation / MRF binding / regulation of androgen receptor signaling pathway / 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 / histone deacetylase complex / positive regulation of cell size / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to fungicide / cellular response to cAMP / transcription repressor complex / erythrocyte differentiation / nuclear receptor coactivator activity / negative regulation of protein binding / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / promoter-specific chromatin binding / HDACs deacetylate histones / 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 / positive regulation of neuron projection development / cerebral cortex development / transcription corepressor activity / cellular response to UV / regulation of protein localization / p53 binding / flavin adenine dinucleotide binding / chromatin organization / 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 gene expression / 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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1880 / : / Helical region in REST corepressor / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Histone lysine-specific demethylase / SWIRM domain / SWIRM domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1880 / : / Helical region in REST corepressor / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Histone lysine-specific demethylase / SWIRM domain / SWIRM domain / SWIRM domain profile. / ATP synthase, gamma subunit, helix hairpin domain / SANT domain profile. / SANT domain / Amine oxidase / Flavin containing amine oxidoreductase / 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
FLAVIN-ADENINE DINUCLEOTIDE / AMMONIUM ION / Lysine-specific histone demethylase 1A / REST corepressor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.57 Å
AuthorsYang, M. / Gocke, C.B. / Luo, X. / Borek, D. / Tomchick, D.R. / Machius, M. / Otwinowski, Z. / Yu, H.
CitationJournal: 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
DepositionJun 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6479
Polymers100,5532
Non-polymers1,0947
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)120.354, 178.222, 234.932
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 / AMINE OXIDASE FLAVIN-CONTAINING DOMAIN PROTEIN 2 / BRAF35-HDAC COMPLEX PROTEIN BHC110


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 / RCOR1 / 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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Non-polymers , 5 types, 85 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT USED CONTAINS A LINKER: (MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFGR) FROM THE CLONING PROCEDURE.

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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: 6.2 Å3/Da / Density % sol: 80.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: VAPOR DIFFUSION, SITTING DROP, 20 DEGREES. DROP: 0.8 MICRO-LITERS OF PROTEIN (10 MG/ML IN 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, 5 MM DTT) PLUS 0.8 MICRO-LITERS OF ...Details: VAPOR DIFFUSION, SITTING DROP, 20 DEGREES. DROP: 0.8 MICRO-LITERS OF PROTEIN (10 MG/ML IN 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, 5 MM DTT) PLUS 0.8 MICRO-LITERS OF CRYSTALLIZATION SOLUTION (0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, 10 MM DTT). RESERVOIR: 1 ML OF CRYSTALLIZATION SOLUTION. CRYSTALS APPEARED WITHIN 12 HOURS AND GREW TO THEIR FINAL SIZE WITHIN 10 DAYS. CRYO-PROTECTION SOLUTION: RESERVOIR SOLUTION PLUS 23 PERCENT (V/V) GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97959
DetectorType: CUSTOM / Detector: CCD / Date: Mar 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.57→49.87 Å / Num. obs: 75117 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 70.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 39.3
Reflection shellResolution: 2.57→2.61 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 60.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.57→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.951 / SU B: 12.484 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1498 2 %RANDOM
Rwork0.203 ---
obs0.204 73416 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.13 Å2
Baniso -1Baniso -2Baniso -3
1-3.11 Å20 Å20 Å2
2---2.12 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.57→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 69 78 6440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226490
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9748802
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8615797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22424.475295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.993151130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3351542
X-RAY DIFFRACTIONr_chiral_restr0.0950.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025635
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22790
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24461
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2210
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5991.54075
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00926437
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3532717
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2114.52365
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: 2.57→2.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 64 -
Rwork0.363 3511 -
obs--61.93 %
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)
14.36470.46052.08313.2490.29186.4921-0.05840.5147-0.2876-0.484-0.1701-0.66230.64491.16580.2284-0.03540.19450.2855-0.0850.1396-0.136676.685250.96445.6154
22.11490.00390.31311.2972-0.07562.3194-0.131-0.321-0.26690.2822-0.3738-0.5228-0.06910.6470.5049-0.20240.0056-0.0441-0.23990.2042-0.261572.236657.956932.5899
32.88664.8436-2.69538.1348-4.56922.81090.0885-0.0846-0.1036-0.1325-0.1194-0.11760.1989-0.13020.03080.5423-0.05870.38060.44530.33960.697431.86412.264658.288
41.7110.4511-0.04192.5658-1.05482.5877-0.0866-0.4718-0.10340.5023-0.2539-0.2103-0.28010.24870.3405-0.1565-0.0237-0.0299-0.29450.0774-0.3963.662261.995737.568
51.4412-1.02990.4453.7026-0.54142.9748-0.03420.23310.0076-0.664-0.3391-0.0202-0.04690.20160.3734-0.13270.0136-0.011-0.4090.0578-0.401661.671865.936512.1176
62.5012.8059-2.98617.8099-7.747910.02020.08970.18650.18390.29410.56940.7977-0.5192-0.6974-0.6591-0.0149-0.04370.25260.1090.23190.231135.414832.395451.2154
76.3515.266-0.07866.5583-0.88444.33740.24680.722-0.63931.53590.5362-2.17870.41130.8131-0.78290.00140.0025-0.00130.00280.00460.000728.1108-13.339670.8583
81.3606-2.5365-4.878422.51341.926220.3797-0.27530.7511-0.1593-0.4349-0.2061-0.5061-0.79150.04910.48140.0591-0.05670.16310.01690.00440.05712.8496-27.134464.6406
99.27066.5133-1.03319.043-2.202830.7383-0.20561.6886-0.1224-1.25430.3703-0.5143-0.52041.0102-0.16470.06740.20260.31080.02960.05920.048315.3989-25.568456.7813
1011.05059.311727.832176.1094-14.539391.24321.1651-0.84272.7574-2.3827-3.08124.1345-0.7005-1.08561.91610.00350.0003-0.00350.00110.0012-0.0014.7064-16.985656.6912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A171 - 274
2X-RAY DIFFRACTION2A275 - 385
3X-RAY DIFFRACTION3A386 - 516
4X-RAY DIFFRACTION4A517 - 775
5X-RAY DIFFRACTION5A776 - 836
6X-RAY DIFFRACTION6B308 - 358
7X-RAY DIFFRACTION7B359 - 383
8X-RAY DIFFRACTION8B384 - 396
9X-RAY DIFFRACTION9B397 - 431
10X-RAY DIFFRACTION10B432 - 440

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