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- PDB-2jxj: NMR structure of the ARID domain from the histone H3K4 demethylas... -

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Basic information

Entry
Database: PDB / ID: 2jxj
TitleNMR structure of the ARID domain from the histone H3K4 demethylase RBP2
ComponentsHistone demethylase JARID1A
KeywordsOXIDOREDUCTASE / ARID domain / Chromatin regulator / Developmental protein / Dioxygenase / Iron / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Transcription / Transcription regulation / Zinc / Zinc-finger
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine4 demethylase / facultative heterochromatin formation / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / enzyme inhibitor activity / regulation of DNA-binding transcription factor activity / histone demethylase activity / methylated histone binding / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones ...[histone H3]-trimethyl-L-lysine4 demethylase / facultative heterochromatin formation / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / enzyme inhibitor activity / regulation of DNA-binding transcription factor activity / histone demethylase activity / methylated histone binding / Chromatin modifications during the maternal to zygotic transition (MZT) / circadian regulation of gene expression / HDMs demethylate histones / chromatin DNA binding / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / chromatin / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / 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 ...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 5A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTu, S. / Yuan, C. / Tsai, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: The ARID domain of the H3K4 demethylase RBP2 binds to a DNA CCGCCC motif
Authors: Tu, S. / Teng, Y.C. / Yuan, C. / Wu, Y.T. / Chan, M.Y. / Cheng, A.N. / Lin, P.H. / Juan, L.J. / Tsai, M.D.
History
DepositionNov 20, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone demethylase JARID1A


Theoretical massNumber of molelcules
Total (without water)10,8371
Polymers10,8371
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 #1closest to the average

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Components

#1: Protein Histone demethylase JARID1A / Jumonji/ARID domain- containing protein 1A / Retinoblastoma-binding protein 2 / RBBP-2


Mass: 10836.677 Da / Num. of mol.: 1 / Fragment: ARID domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JARID1A, RBBP2, RBP2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P29375, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D 1H-15N NOESY
1323D 1H-13C NOESY
1413D HNHA
1513D HNHB
1613D CBCA(CO)NH
1713D 1H-15N TOCSY
1813D HNCO
1923D (H)CCH-TOCSY
11023D (H)CCH-COSY
11113D HNCA
11213D HN(CO)CA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 13C; U-100% 15N] protein, 50 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-100% 13C; U-100% 15N] protein, 50 mM sodium phosphate, 100 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMentity[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate1
100 mMsodium chloride1
0.4 mMentity[U-100% 13C; U-100% 15N]2
50 mMsodium phosphate2
100 mMsodium chloride2
Sample conditionsIonic strength: ~200 mM salt / pH: 6.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRViewJohnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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