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- PDB-2l3d: The solution structure of the short form SWIRM domain of LSD1 -

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Basic information

Entry
Database: PDB / ID: 2l3d
TitleThe solution structure of the short form SWIRM domain of LSD1
ComponentsLysine-specific histone demethylase 1A
KeywordsTRANSCRIPTION / LSD1 / SWIRM
Function / homology
Function and homology information


positive regulation of histone ubiquitination / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin assembly / histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / telomeric repeat-containing RNA binding / demethylase activity / protein demethylation / positive regulation of neural precursor cell proliferation / muscle cell development ...positive regulation of histone ubiquitination / guanine metabolic process / regulation of DNA methylation-dependent heterochromatin assembly / histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / telomeric repeat-containing RNA binding / demethylase activity / protein demethylation / positive regulation of neural precursor cell proliferation / muscle cell development / histone H3-methyl-lysine-4 demethylase activity / neuron maturation / positive regulation of stem cell proliferation / alternative mRNA splicing, via spliceosome / negative regulation of histone H3-K9 methylation / DNA repair complex / histone H3-K4 demethylation / regulation of androgen receptor signaling pathway / MRF binding / positive regulation of cell size / negative regulation of histone H3-K4 methylation / regulation of double-strand break repair via homologous recombination / nuclear androgen receptor binding / positive regulation of neuroblast proliferation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of chromatin binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / histone H3-K9 demethylation / histone H3-methyl-lysine-9 demethylase activity / negative regulation of DNA binding / response to fungicide / histone demethylase activity / cerebral cortex development / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / HDACs deacetylate histones / cellular response to cAMP / positive regulation of neuron projection development / Regulation of PTEN gene transcription / nuclear receptor coactivator activity / promoter-specific chromatin binding / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / cellular response to gamma radiation / cellular response to UV / negative regulation of protein binding / positive regulation of cold-induced thermogenesis / regulation of protein localization / negative regulation of DNA-binding transcription factor activity / p53 binding / flavin adenine dinucleotide binding / Factors involved in megakaryocyte development and platelet production / positive regulation of DNA-binding transcription factor activity / Potential therapeutics for SARS / DNA-binding transcription factor binding / Estrogen-dependent gene expression / chromatin organization / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / transcription regulator complex / oxidoreductase activity / negative regulation of transcription, DNA-templated / chromatin / chromatin binding / 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 / nucleus
Similarity search - Function
Histone lysine-specific demethylase / SWIRM domain / SWIRM domain profile. / SWIRM domain / Amine oxidase / Flavin containing amine oxidoreductase / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / FAD/NAD(P)-binding domain superfamily / Arc Repressor Mutant, subunit A ...Histone lysine-specific demethylase / SWIRM domain / SWIRM domain profile. / SWIRM domain / Amine oxidase / Flavin containing amine oxidoreductase / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / FAD/NAD(P)-binding domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Lysine-specific histone demethylase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsLiu, C. / Lo, K. / Zhu, G. / Sze, K.
CitationJournal: To be Published
Title: The chemical shift assignment of the SWIRM domain of LSD1
Authors: Liu, C. / Luo, R. / Sze, K.
History
DepositionSep 13, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine-specific histone demethylase 1A


Theoretical massNumber of molelcules
Total (without water)11,7651
Polymers11,7651
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Lysine-specific histone demethylase 1A


Mass: 11765.438 Da / Num. of mol.: 1 / Fragment: SWIRM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60341

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D C(CO)NH
1923D (H)CCH-TOCSY
11023D (H)CCH-COSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM [U-100% 13C; U-100% 15N] SWIRM-1, 50mM sodium phosphate-2, 50mM sodium chloride-3, 2mM DTT-4, 1mM EDTA-5, 90% H2O/10% D2O90% H2O/10% D2O
20.8mM SWIRM-6, 50mM sodium phosphate-7, 50mM sodium chloride-8, 2mM DTT-9, 1mM EDTA-10, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMSWIRM-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
50 mMsodium chloride-31
2 mMDTT-41
1 mMEDTA-51
0.8 mMSWIRM-62
50 mMsodium phosphate-72
50 mMsodium chloride-82
2 mMDTT-92
1 mMEDTA-102
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPARKYGoddarddata analysis
SPARKYGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AMBERrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: Amber
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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