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- PDB-8ulz: LSD1-CoREST in complex with T18 and SNAG peptide -

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Basic information

Entry
Database: PDB / ID: 8ulz
TitleLSD1-CoREST in complex with T18 and SNAG peptide
Components
  • Lysine-specific histone demethylase 1A
  • REST corepressor 1
  • Zinc finger protein SNAI1
KeywordsOXIDOREDUCTASE/INHIBITOR / Epigenetics / Histone demethylase / Drug resistance / Covalent inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / Regulation of CDH11 gene transcription / negative regulation of vitamin D biosynthetic process / epithelial cell migration / epithelial to mesenchymal transition involved in endocardial cushion formation / trophoblast giant cell differentiation / heterochromatin organization / positive regulation of megakaryocyte differentiation ...negative regulation of cell differentiation involved in embryonic placenta development / cartilage morphogenesis / left/right pattern formation / Regulation of CDH11 gene transcription / negative regulation of vitamin D biosynthetic process / epithelial cell migration / epithelial to mesenchymal transition involved in endocardial cushion formation / trophoblast giant cell differentiation / heterochromatin organization / positive regulation of megakaryocyte differentiation / guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / Epithelial-Mesenchymal Transition (EMT) during gastrulation / protein demethylase activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / neuron maturation / muscle cell development / positive regulation of neural precursor cell proliferation / histone H3K9 demethylase activity / MRF binding / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of androgen receptor signaling pathway / aortic valve morphogenesis / DNA repair complex / histone demethylase activity / regulation of bicellular tight junction assembly / hair follicle morphogenesis / 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 / E-box binding / histone methyltransferase complex / negative regulation of DNA damage response, signal transduction by p53 class mediator / pericentric heterochromatin / roof of mouth development / mesoderm formation / histone deacetylase complex / epithelial to mesenchymal transition / positive regulation of cell size / canonical Wnt signaling pathway / positive regulation of epithelial to mesenchymal transition / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Notch signaling pathway / positive regulation of protein ubiquitination / transcription repressor complex / cellular response to cAMP / epigenetic regulation of gene expression / Regulation of PTEN gene transcription / erythrocyte differentiation / HDMs demethylate histones / RNA polymerase II transcription regulatory region sequence-specific DNA binding / HDACs deacetylate histones / promoter-specific chromatin binding / cellular response to gamma radiation / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / positive regulation of neuron projection development / cerebral cortex development / protein modification process / DNA-binding transcription repressor activity, RNA polymerase II-specific / kinase binding / fibrillar center / sequence-specific double-stranded DNA binding / osteoblast differentiation / cellular response to UV / p53 binding / transcription corepressor activity / flavin adenine dinucleotide binding / regulation of protein localization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / chromatin organization / transcription regulator complex / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / chromosome, telomeric region / oxidoreductase activity / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II
Similarity search - Function
: / C2H2-type zinc finger / : / Helical region in REST corepressor / : / Histone lysine-specific demethylase / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 ...: / C2H2-type zinc finger / : / Helical region in REST corepressor / : / Histone lysine-specific demethylase / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / 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 / Zinc finger, C2H2 type / SANT/Myb domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / Lysine-specific histone demethylase 1A / Zinc finger protein SNAI1 / REST corepressor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsCaroli, J. / Mattevi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG19808 Italy
CitationJournal: To Be Published
Title: Distal drug resistance mutations promote covalent inhibitor-adduct Grob fragmentation in LSD1
Authors: Caroli, J. / Mattevi, A.
History
DepositionOct 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Zinc finger protein SNAI1
A: Lysine-specific histone demethylase 1A
B: REST corepressor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6534
Polymers112,6143
Non-polymers1,0391
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-43 kcal/mol
Surface area37680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.371, 177.771, 234.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein/peptide Zinc finger protein SNAI1 / Protein snail homolog 1 / Protein sna


Mass: 1102.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAI1, SNAH / Production host: Escherichia coli (E. coli) / References: UniProt: O95863
#2: Protein Lysine-specific histone demethylase 1A / BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2 / ...BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2 / [histone H3]-dimethyl-L-lysine(4) FAD-dependent demethylase 1A


Mass: 95051.633 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 (E. coli)
References: UniProt: O60341, [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase
#3: Protein REST corepressor 1 / Protein CoREST


Mass: 16459.742 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 (E. coli) / References: UniProt: Q9UKL0
#4: Chemical ChemComp-YAO / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-(3-benzamidophenyl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)


Mass: 1038.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H48N10O17P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 293 K / Method: vapor diffusion, hanging drop / Details: 1.2 Sodium Potassium Tartrate, 100 mM ADA pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 2.808→106.427 Å / Num. obs: 41073 / % possible obs: 67 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.04 / Rrim(I) all: 0.149 / Net I/σ(I): 13.3 / Num. measured all: 562400
Reflection shellResolution: 2.808→3.112 Å / % possible obs: 12.7 % / Redundancy: 13.9 % / Rmerge(I) obs: 1.932 / Num. measured all: 28662 / Num. unique obs: 2055 / Rpim(I) all: 0.53 / Rrim(I) all: 2.004 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→65.49 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2305 1997 5.36 %
Rwork0.1989 --
obs0.2006 37234 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.32→65.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6328 0 72 0 6400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126537
X-RAY DIFFRACTIONf_angle_d1.4788867
X-RAY DIFFRACTIONf_dihedral_angle_d12.555927
X-RAY DIFFRACTIONf_chiral_restr0.08990
X-RAY DIFFRACTIONf_plane_restr0.0091144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.40.3711400.33092483X-RAY DIFFRACTION100
3.4-3.490.29481410.2822471X-RAY DIFFRACTION100
3.49-3.590.29451420.24932508X-RAY DIFFRACTION100
3.59-3.710.27831420.22822497X-RAY DIFFRACTION100
3.71-3.840.23981410.22492496X-RAY DIFFRACTION100
3.84-40.25531430.21282502X-RAY DIFFRACTION100
4-4.180.24471410.21052497X-RAY DIFFRACTION99
4.18-4.40.24051370.19082420X-RAY DIFFRACTION96
4.4-4.670.23661430.18232513X-RAY DIFFRACTION100
4.67-5.030.20511420.17752522X-RAY DIFFRACTION100
5.04-5.540.22921430.19792535X-RAY DIFFRACTION100
5.54-6.340.24511460.19612562X-RAY DIFFRACTION100
6.34-7.990.19351460.18582577X-RAY DIFFRACTION100
7.99-65.490.19161500.17152654X-RAY DIFFRACTION99

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