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- PDB-6wc6: Crystal structure of a truncated LSD1:CoREST in the presence of a... -

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Basic information

Entry
Database: PDB / ID: 6wc6
TitleCrystal structure of a truncated LSD1:CoREST in the presence of an LSD1-NT peptide
Components
  • LSD1-NT peptide
  • Lysine-specific histone demethylase 1A
  • REST corepressor 1
KeywordsOXIDOREDUCTASE / LSD1/CoREST / N terminal peptide
Function / homology
Function and homology information


positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [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 / muscle cell development ...positive regulation of megakaryocyte differentiation / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin formation / protein demethylation / [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 / muscle cell development / neuron maturation / positive regulation of neural precursor cell proliferation / 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 / histone deacetylase complex / positive regulation of cell size / histone demethylase activity / positive regulation of epithelial to mesenchymal transition / response to fungicide / cellular response to cAMP / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription repressor complex / erythrocyte differentiation / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / cellular response to gamma radiation / cerebral cortex development / positive regulation of neuron projection development / transcription corepressor activity / regulation of protein localization / cellular response to UV / p53 binding / chromatin organization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / flavin adenine dinucleotide binding / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / chromosome, telomeric region / oxidoreductase activity / transcription coactivator activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / Helical region in REST corepressor / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Histone lysine-specific demethylase / SWIRM domain / SWIRM domain / SWIRM domain profile. ...: / Helical region in REST corepressor / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / Histone lysine-specific demethylase / SWIRM domain / SWIRM domain / SWIRM domain profile. / 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 / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Lysine-specific histone demethylase 1A / REST corepressor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsReiter, N.J. / Zeng, D. / Senanayaka, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120572 United States
CitationJournal: To Be Published
Title: Identification of structure and nucleosome binding within the N-terminus of lysine specific demethylase 1
Authors: Zeng, D. / Senanayaka, D. / Brown, B.P. / Luka, Z. / Martin, W.J. / Moore, K.I. / Patel, R. / Pakhomova, S. / Meiler, J. / Reiter, N.J.
History
DepositionMar 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: REST corepressor 1
C: LSD1-NT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0244
Polymers91,2383
Non-polymers7861
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.783, 179.164, 234.907
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
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

#1: Protein Lysine-specific histone demethylase 1A / BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2


Mass: 74126.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60341, Oxidoreductases
#2: Protein REST corepressor 1 / Protein CoREST


Mass: 15317.435 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RCOR1, KIAA0071, RCOR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UKL0
#3: Protein/peptide LSD1-NT peptide / Lysine-specific histone demethylase 1A


Mass: 1793.991 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A, AOF2, KDM1, KIAA0601, LSD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60341
#4: Chemical ChemComp-FAD / 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
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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: The LSD1-CoREST complex 10mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 1 mM TCEP) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, ...Details: The LSD1-CoREST complex 10mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 1 mM TCEP) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, 100 mM Na-citrate, pH 5.6, 5 mM TCEP]. When get crystals, soak the crystals within 5mM LSD1-NT peptide.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.1→142.46 Å / Num. obs: 46959 / % possible obs: 99.9 % / Redundancy: 15 % / Biso Wilson estimate: 83.45 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.7
Reflection shellResolution: 3.1→3.21 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4642 / CC1/2: 0.764

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Processing

Software
NameVersionClassification
REFMAC5-3.1refinement
PHENIX1.16_3549refinement
xia2data reduction
DIALSdata scaling
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XBF

4xbf


Resolution: 3.1→100.72 Å / SU ML: 0.4494 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8876
RfactorNum. reflection% reflection
Rfree0.2358 2290 4.88 %
Rwork0.2161 --
obs0.2171 46920 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 101.89 Å2
Refinement stepCycle: LAST / Resolution: 3.1→100.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6417 0 53 0 6470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00286603
X-RAY DIFFRACTIONf_angle_d0.57858951
X-RAY DIFFRACTIONf_chiral_restr0.04071000
X-RAY DIFFRACTIONf_plane_restr0.00371155
X-RAY DIFFRACTIONf_dihedral_angle_d3.25593995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.140.45351430.45672935X-RAY DIFFRACTION99.87
3.14-3.170.49561690.41872765X-RAY DIFFRACTION99.86
3.17-3.210.44551350.40222871X-RAY DIFFRACTION99.9
3.21-3.250.38731290.35792900X-RAY DIFFRACTION99.93
3.25-3.290.35571410.32862846X-RAY DIFFRACTION99.93
3.29-3.340.32061300.31232864X-RAY DIFFRACTION99.93
3.34-3.390.34711410.3042896X-RAY DIFFRACTION100
3.39-3.440.30121480.28792814X-RAY DIFFRACTION99.76
3.44-3.490.29511520.2782861X-RAY DIFFRACTION99.8
3.49-3.550.28551540.25832855X-RAY DIFFRACTION99.93
3.55-3.610.26911520.25192860X-RAY DIFFRACTION100
3.61-3.680.25551550.24522846X-RAY DIFFRACTION99.93
3.68-3.750.25871580.23072789X-RAY DIFFRACTION99.83
3.75-3.820.24271540.22272855X-RAY DIFFRACTION99.97
3.82-3.910.23591530.20532880X-RAY DIFFRACTION99.97
3.91-40.23341420.19652861X-RAY DIFFRACTION100
4-4.10.2181530.1912856X-RAY DIFFRACTION100
4.1-4.210.25721520.18342857X-RAY DIFFRACTION100
4.21-4.330.17161370.16612866X-RAY DIFFRACTION100
4.33-4.470.18111390.16192825X-RAY DIFFRACTION99.93
4.47-4.630.18991590.16262845X-RAY DIFFRACTION100
4.63-4.820.17551450.16552878X-RAY DIFFRACTION100
4.82-5.040.20171350.16722855X-RAY DIFFRACTION100
5.04-5.30.25851360.18472895X-RAY DIFFRACTION100
5.3-5.630.21411450.19642832X-RAY DIFFRACTION100
5.63-6.070.20571330.21732854X-RAY DIFFRACTION100
6.07-6.680.23021280.21162907X-RAY DIFFRACTION100
6.68-7.640.24441550.2072847X-RAY DIFFRACTION100
7.64-9.630.19191710.17422822X-RAY DIFFRACTION100
9.63-100.720.17841510.20832836X-RAY DIFFRACTION98.71
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)
10.2892933607180.603159257341-0.2321767015791.39936572475-0.7177177525510.4776259078430.00159311237932-0.160103657173-0.2293817856180.185832166059-0.179262393386-0.141604384140.1078250434650.1186293162670.2002604465870.8231930615360.07730970234560.1001894087590.6269540016850.1143545063970.635088573876182.54344542550.349373081333.8384634517
20.6099273323080.968792413681-0.4422171278921.25635494337-0.5333382700320.2372841852480.04579891700060.2048208282290.131226811982-0.401393993732-0.150280253224-0.1549961341730.244631563894-0.05507534041290.1115273113261.086619152940.08289120316190.2526971685521.015432409150.1303765282730.875550285381146.273798976-0.98847751243658.158423213
30.003087426858570.00371499763361-0.002223493606640.005862806882620.003151486927790.00855794001894-0.2099611199580.05541930750420.239695833644-0.0100280664686-0.0357983479037-0.160569429793-0.2319744329730.248062941990.1883933336282.204970524130.12051328037-0.1348626882341.421316594440.1636570928541.54791223716187.1348020580.972840049844.5338071609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 171:901)
2X-RAY DIFFRACTION2(chain B and resseq 308:440)
3X-RAY DIFFRACTION3(chain C and resseq 4:18)

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