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- PDB-8q1g: LSD1-CoREST bound to Acetylated K14 of Histone H3 -

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Basic information

Entry
Database: PDB / ID: 8q1g
TitleLSD1-CoREST bound to Acetylated K14 of Histone H3
Components
  • Histone H3.3C
  • Lysine-specific histone demethylase 1A
  • REST corepressor 1RCOR1
KeywordsOXIDOREDUCTASE / Histone Code / Demethylase / Flavin
Function / homology
Function and homology information


positive regulation of megakaryocyte differentiation / guanine metabolic process / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / regulation of DNA methylation-dependent heterochromatin formation / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development ...positive regulation of megakaryocyte differentiation / guanine metabolic process / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / demethylase activity / regulation of DNA methylation-dependent heterochromatin formation / telomeric repeat-containing RNA binding / histone H3K4 demethylase activity / muscle cell development / positive regulation of neural precursor cell proliferation / neuron maturation / 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 / nucleosomal DNA binding / histone demethylase activity / 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 / promoter-specific chromatin binding / HDACs deacetylate histones / euchromatin / 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 / cerebral cortex development / positive regulation of neuron projection development / structural constituent of chromatin / transcription corepressor activity / cellular response to UV / regulation of protein localization / nucleosome / p53 binding / flavin adenine dinucleotide binding / positive regulation of cold-induced thermogenesis / chromatin organization / Factors involved in megakaryocyte development and platelet production / positive regulation of cell growth / 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 / protein heterodimerization 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
: / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / FAD/NAD(P)-binding domain superfamily / 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: 2.6 Å
AuthorsBarone, M. / Mattevi, A.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della RicercaFISR MEDYCA Italy
CitationJournal: To Be Published
Title: Uncoupling Histone Modification Crosstalk by Engineering Lysine Demethylase LSD1
Authors: Kwangwoon, L. / Barone, M. / Waterbury, A.L. / Jiang, H. / Nam, E. / Whedon, S.D. / Wang, Z.A. / Caroli, J. / Ibeabuchi, B. / Neal, K. / Dhoondia, Z. / Kuroda, M. / Liau, 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

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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: Histone H3.3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6154
Polymers103,8293
Non-polymers7861
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-57 kcal/mol
Surface area36830 Å2
Unit cell
Length a, b, c (Å)119.508, 179.693, 232.015
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 / BRAF35-HDAC complex protein BHC110 / Flavin-containing amine oxidase domain-containing protein 2


Mass: 81279.438 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 (bacteria) / References: UniProt: O60341, Oxidoreductases
#2: Protein REST corepressor 1 / RCOR1 / 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: 2304.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6NXT2
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
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: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Sodium Tartrate 1.2M, 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: Sep 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2.6→48.73 Å / Num. obs: 74979 / % possible obs: 98 % / Redundancy: 4.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.052 / Rrim(I) all: 0.114 / Χ2: 0.99 / Net I/σ(I): 8.8 / Num. measured all: 338452
Reflection shellResolution: 2.6→2.65 Å / % possible obs: 97 % / Redundancy: 4.2 % / Rmerge(I) obs: 2.926 / Num. measured all: 18223 / Num. unique obs: 4320 / CC1/2: 0.138 / Rpim(I) all: 1.621 / Rrim(I) all: 3.372 / Χ2: 1 / Net I/σ(I) obs: 0.5

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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: 2.6→48.73 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 1949 2.67 %
Rwork0.2219 --
obs0.2227 72987 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6410 0 53 8 6471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016597
X-RAY DIFFRACTIONf_angle_d1.2018946
X-RAY DIFFRACTIONf_dihedral_angle_d11.289886
X-RAY DIFFRACTIONf_chiral_restr0.0591001
X-RAY DIFFRACTIONf_plane_restr0.011154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.49051120.46894076X-RAY DIFFRACTION77
2.67-2.740.48711160.4344316X-RAY DIFFRACTION82
2.74-2.820.43191400.40615038X-RAY DIFFRACTION95
2.82-2.910.42021430.39935217X-RAY DIFFRACTION98
2.91-3.010.36621420.36445192X-RAY DIFFRACTION98
3.01-3.130.35871440.33625242X-RAY DIFFRACTION98
3.13-3.280.29991420.29725201X-RAY DIFFRACTION98
3.28-3.450.30941450.26185253X-RAY DIFFRACTION98
3.45-3.660.26761430.24655218X-RAY DIFFRACTION98
3.66-3.950.2581430.21695176X-RAY DIFFRACTION97
3.95-4.340.23251420.18585191X-RAY DIFFRACTION97
4.34-4.970.20821450.17375318X-RAY DIFFRACTION98
4.97-6.260.25321460.19915284X-RAY DIFFRACTION98
6.26-48.730.18631460.16355316X-RAY DIFFRACTION95

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