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- PDB-8q1h: LSD1 Y391K-CoREST bound to Histone H3 N-terminal tail -

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Basic information

Entry
Database: PDB / ID: 8q1h
TitleLSD1 Y391K-CoREST bound to Histone H3 N-terminal tail
Components
  • Histone H3.3C
  • Lysine-specific histone demethylase 1A
  • REST corepressor 1
KeywordsOXIDOREDUCTASE / Histone Code / Demethylase / Flavin
Function / homology
Function and homology information


positive regulation of megakaryocyte differentiation / guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / 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 / neuron maturation ...positive regulation of megakaryocyte differentiation / guanine metabolic process / negative regulation of transcription initiation-coupled chromatin remodeling / 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 / neuron maturation / muscle cell development / positive regulation of neural precursor cell proliferation / MRF binding / regulation of androgen receptor signaling pathway / DNA repair complex / negative regulation of DNA binding / nucleosomal DNA binding / 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 H3K9 demethylase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase complex / histone demethylase activity / positive regulation of cell size / positive regulation of epithelial to mesenchymal transition / response to fungicide / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to cAMP / transcription repressor complex / negative regulation of protein binding / erythrocyte differentiation / epigenetic regulation of gene expression / Regulation of PTEN gene transcription / positive regulation of protein ubiquitination / HDACs deacetylate histones / negative regulation of DNA-binding transcription factor activity / promoter-specific chromatin binding / euchromatin / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / cellular response to gamma radiation / HDMs demethylate histones / cerebral cortex development / positive regulation of neuron projection development / transcription corepressor activity / structural constituent of chromatin / cellular response to UV / p53 binding / nucleosome / flavin adenine dinucleotide binding / regulation of protein localization / chromatin organization / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / positive regulation of cell growth / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / Estrogen-dependent gene expression / Potential therapeutics for SARS / transcription coactivator activity / chromosome, telomeric region / oxidoreductase activity / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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 / : / Histone lysine-specific demethylase / ELM2 domain / ELM2 domain / ELM2 domain profile. / ELM2 / SWIRM domain / SWIRM domain ...: / 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 / SANT/Myb domain / Histone H3 signature 1. / Homeobox-like domain superfamily / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Lysine-specific histone demethylase 1A / Histone H3.3C / REST corepressor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBarone, M. / Mattevi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della RicercaFISR MEDYCA Italy
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1.
Authors: Lee, K. / Barone, M. / Waterbury, A.L. / Jiang, H. / Nam, E. / DuBois-Coyne, S.E. / Whedon, S.D. / Wang, Z.A. / Caroli, J. / Neal, K. / Ibeabuchi, B. / Dhoondia, Z. / Kuroda, M.I. / Liau, B. ...Authors: Lee, K. / Barone, M. / Waterbury, A.L. / Jiang, H. / Nam, E. / DuBois-Coyne, S.E. / Whedon, S.D. / Wang, Z.A. / Caroli, J. / Neal, K. / Ibeabuchi, B. / Dhoondia, Z. / Kuroda, M.I. / Liau, B.B. / Beck, S. / Mattevi, A. / Cole, P.A.
History
DepositionJul 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 12, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine-specific histone demethylase 1A
B: REST corepressor 1
C: Histone H3.3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5394
Polymers103,7543
Non-polymers7861
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9000 Å2
ΔGint-57 kcal/mol
Surface area37440 Å2
Unit cell
Length a, b, c (Å)118.061, 179.354, 233.055
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 Lysine-specific histone demethylase 1A


Mass: 81245.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM1A / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O60341
#2: Protein REST corepressor 1 / Protein CoREST


Mass: 20244.824 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 (bacteria) / References: UniProt: Q9UKL0
#3: Protein/peptide Histone H3.3C / Histone H3.5


Mass: 2263.666 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6NXT2
#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
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

CrystalDensity Matthews: 5.95 Å3/Da / Density % sol: 79.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Sodium Tartrate 1.2 M, ADA 0.1M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2.9→48.86 Å / Num. obs: 54837 / % possible obs: 99.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 81 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.072 / Rrim(I) all: 0.152 / Χ2: 1.01 / Net I/σ(I): 8
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.786 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4461 / CC1/2: 0.383 / Rpim(I) all: 0.972 / Rrim(I) all: 2.043 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→48.86 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 1992 3.65 %
Rwork0.2326 --
obs0.2334 54585 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6377 0 53 0 6430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096562
X-RAY DIFFRACTIONf_angle_d1.1818897
X-RAY DIFFRACTIONf_dihedral_angle_d9.267876
X-RAY DIFFRACTIONf_chiral_restr0.056998
X-RAY DIFFRACTIONf_plane_restr0.0111146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.49041380.45933619X-RAY DIFFRACTION97
2.97-3.050.45741410.41923735X-RAY DIFFRACTION99
3.05-3.140.4291400.38163693X-RAY DIFFRACTION99
3.14-3.240.38511420.33353744X-RAY DIFFRACTION100
3.24-3.360.33231420.30283752X-RAY DIFFRACTION100
3.36-3.490.37541420.29343732X-RAY DIFFRACTION100
3.49-3.650.33051410.27823751X-RAY DIFFRACTION99
3.65-3.850.26761430.24923752X-RAY DIFFRACTION100
3.85-4.090.22871420.22293750X-RAY DIFFRACTION99
4.09-4.40.23051410.19343737X-RAY DIFFRACTION99
4.4-4.840.20551430.18393773X-RAY DIFFRACTION100
4.85-5.550.21681440.2063808X-RAY DIFFRACTION100
5.55-6.980.24031440.2163840X-RAY DIFFRACTION100
6.98-48.860.16921490.17413907X-RAY DIFFRACTION98

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