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- PDB-2jrz: Solution structure of the Bright/ARID domain from the human JARID... -

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Basic information

Entry
Database: PDB / ID: 2jrz
TitleSolution structure of the Bright/ARID domain from the human JARID1C protein.
ComponentsHistone demethylase JARID1C
KeywordsOXIDOREDUCTASE / JARID1C / Bright/ARID domain / helical / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


[histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K4 demethylase activity / histone demethylase activity / HDMs demethylate histones / rhythmic process / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription ...[histone H3]-trimethyl-L-lysine4 demethylase / histone H3K4me/H3K4me2/H3K4me3 demethylase activity / histone H3K4 demethylase activity / histone demethylase activity / HDMs demethylate histones / rhythmic process / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
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 superfamily ...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 5C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsEnsemble of 20 lowest energy NMR structures of the Bright/ARID domain from the human JARID1C ...Ensemble of 20 lowest energy NMR structures of the Bright/ARID domain from the human JARID1C protein (Smcx homolog, X chromosome).
AuthorsKoehler, C. / Bishop, S. / Dowler, E.F. / Diehl, A. / Schmieder, P. / Leidert, M. / Sundstrom, M. / Arrowsmith, C.H. / Wiegelt, J. / Edwards, A. ...Koehler, C. / Bishop, S. / Dowler, E.F. / Diehl, A. / Schmieder, P. / Leidert, M. / Sundstrom, M. / Arrowsmith, C.H. / Wiegelt, J. / Edwards, A. / Oschkinat, H. / Ball, L.J. / Structural Genomics Consortium (SGC)
CitationJournal: Biomol.Nmr Assign. / Year: 2008
Title: Backbone and sidechain 1H, 13C and 15N resonance assignments of the Bright/ARID domain from the human JARID1C (SMCX) protein.
Authors: Koehler, C. / Bishop, S. / Dowler, E.F. / Schmieder, P. / Diehl, A. / Oschkinat, H. / Ball, L.J.
History
DepositionJun 29, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 999sequence Author stated that Q175 in UNP entry P41229 is not present in this protein, and the ...sequence Author stated that Q175 in UNP entry P41229 is not present in this protein, and the protein is an isoform of P41229.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone demethylase JARID1C


Theoretical massNumber of molelcules
Total (without water)13,7491
Polymers13,7491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone demethylase JARID1C / Jumonji/ARID domain-containing protein 1C / Protein SmcX / Protein Xe169


Mass: 13748.627 Da / Num. of mol.: 1 / Fragment: Bright, ARID domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JARID1C, DXS1272E, SMCX, XE169 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta DE3
References: UniProt: P41229, 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
Details: Ensemble of 20 lowest energy NMR structures of the Bright/ARID domain from the human JARID1C protein (Smcx homolog, X chromosome).
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1143D CBCA(CO)NH
1243D CBCANH
1312D 1H-15N HSQC
1422D 1H-13C HSQC
1543D HNCA
1643D HN(CA)CO
1743D HBHA(CO)NH
1843D H(CCCO)NH-TOCSY
194(H)CC(CO)NH-TOCSY
11023D (H)CCH-TOCSY
11123D (H)CCH-COSY
11213D 1H-15N NOESY
11323D 1H-13C NOESY
11443D 1H-13C NOESY
11532D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] JARID1C, 50 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] JARID1C, 50 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 5 mM DTT, 100% D2O100% D2O
31 mM [U-100% 15N] JARID1C, 50 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 5 mM DTT, 100% D2O100% D2O
41 mM [U-13C; U-15N] JARID1C, 50 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMJARID1C[U-100% 15N]1
50 mMsodium phosphate1
50 mMsodium chloride1
0.02 %sodium azide1
5 mMDTT1
1 mMJARID1C[U-13C; U-15N]2
50 mMsodium phosphate2
50 mMsodium chloride2
0.02 %sodium azide2
5 mMDTT2
1 mMJARID1C[U-100% 15N]3
50 mMsodium phosphate3
50 mMsodium chloride3
0.02 %sodium azide3
5 mMDTT3
1 mMJARID1C[U-13C; U-15N]4
50 mMsodium phosphate4
50 mMsodium chloride4
0.02 %sodium azide4
5 mMDTT4
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 297 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6 and 3.1Bruker Biospincollection
XwinNMR2.6 and 3.1Bruker Biospinprocessing
Sparky3.1Goddarddata analysis
Sparky3.1Goddardpeak picking
Sparky3.1Goddardchemical shift assignment
CYANA2,0Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.14Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readreffnement in explicit water
TALOSCornilescu, Delaglio and Baxdihedral angle estimation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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