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- PDB-2lm1: Solution NMR Structure of Lysine-specific demethylase lid from Dr... -

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Basic information

Entry
Database: PDB / ID: 2lm1
TitleSolution NMR Structure of Lysine-specific demethylase lid from Drosophila melanogaster, Northeast Structural Genomics Consortium Target FR824D
ComponentsLysine-specific demethylase lid
KeywordsDNA BINDING PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes / CEBS
Function / homology
Function and homology information


TFAP2 (AP-2) family regulates transcription of cell cycle factors / histone H4R3 demethylase activity / male germ-line stem cell population maintenance / synaptonemal complex organization / oocyte karyosome formation / larval somatic muscle development / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / negative regulation of stem cell differentiation / enzyme inhibitor activity ...TFAP2 (AP-2) family regulates transcription of cell cycle factors / histone H4R3 demethylase activity / male germ-line stem cell population maintenance / synaptonemal complex organization / oocyte karyosome formation / larval somatic muscle development / [histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / negative regulation of stem cell differentiation / enzyme inhibitor activity / Sin3-type complex / locomotor rhythm / histone reader activity / circadian regulation of gene expression / chromatin organization / chromatin remodeling / chromatin / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / metal ion binding / nucleus
Similarity search - Function
ARID DNA-binding domain / : / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain ...ARID DNA-binding domain / : / : / Lysine-specific demethylase 5, C-terminal helical domain / Lysine-specific demethylase-like domain / PLU-1-like protein / Zinc finger, C5HC2-type / C5HC2 zinc finger / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / DNA polymerase; domain 1 / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Lysine-specific demethylase 5
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsMills, J.L. / Lee, D. / Kohan, E. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Kusch, T. / Montelione, G.T. / Szyperski, T. ...Mills, J.L. / Lee, D. / Kohan, E. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Kusch, T. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG) / Chaperone-Enabled Studies of Epigenetic Regulation Enzymes (CEBS)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target FR824D
Authors: Mills, J.L. / Lee, D. / Kohan, E. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionNov 18, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Lysine-specific demethylase lid


Theoretical massNumber of molelcules
Total (without water)12,4941
Polymers12,4941
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Lysine-specific demethylase lid / Histone demethylase lid / Jumonji/ARID domain-containing protein lid / Protein little imaginal ...Histone demethylase lid / Jumonji/ARID domain-containing protein lid / Protein little imaginal disks / Retinoblastoma-binding protein 2 homolog


Mass: 12493.500 Da / Num. of mol.: 1 / Fragment: ARID domain residues 214-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG9088, lid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q9VMJ7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D (H)CCH-COSY
1613D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1722D 1H-13C HSQC
1812D 1H-13C HSQC aliphatic
1912D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] FR824D, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM TRIS, 95% H2O/5% D2O95% H2O/5% D2O
21.3 mM [U-5% 13C; U-100% 15N] FR824D, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM TRIS, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMFR824D-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
5 mMDTT-31
0.02 %sodium azide-41
10 mMTRIS-51
1.3 mMFR824D-6[U-5% 13C; U-100% 15N]2
100 mMsodium chloride-72
5 mMDTT-82
0.02 %sodium azide-92
10 mMTRIS-102
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinemen,structure solution,geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement,geometry optimization,structure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis,chemical shift assignment
PROSAGuntertprocessing
CARAKeller and Wuthrichdata analysis,peak picking,chemical shift assignment
VnmrJVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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