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- PDB-2rq5: Solution structure of the AT-rich interaction domain (ARID) of Ju... -

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Basic information

Entry
Database: PDB / ID: 2rq5
TitleSolution structure of the AT-rich interaction domain (ARID) of Jumonji/JARID2
ComponentsProtein Jumonji
KeywordsTRANSCRIPTION / PROTEIN / Developmental protein / Nucleus / Repressor / Transcription regulation
Function / homology
Function and homology information


: / : / : / PRC2 methylates histones and DNA / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation / ESC/E(Z) complex / histone methyltransferase complex / transcription factor binding / spleen development ...: / : / : / PRC2 methylates histones and DNA / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation / ESC/E(Z) complex / histone methyltransferase complex / transcription factor binding / spleen development / thymus development / liver development / cellular response to leukemia inhibitory factor / stem cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of cell population proliferation / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / nucleus
Similarity search - Function
ARID DNA-binding domain / Zinc finger, C5HC2-type / C5HC2 zinc finger / 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 ...ARID DNA-binding domain / Zinc finger, C5HC2-type / C5HC2 zinc finger / 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. / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKusunoki, H. / Kohno, T.
CitationJournal: Proteins / Year: 2009
Title: Solution structure of the AT-rich interaction domain of Jumonji/JARID2
Authors: Kusunoki, H. / Takeuchi, T. / Kohno, T.
History
DepositionFeb 6, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINE METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Jumonji


Theoretical massNumber of molelcules
Total (without water)13,9791
Polymers13,9791
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 Protein Jumonji / Jumonji/ARID domain-containing protein 2


Mass: 13979.377 Da / Num. of mol.: 1 / Fragment: ARID domain, UNP residues 615-730
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Jmj / Production host: Escherichia coli (E. coli) / References: UniProt: Q62315

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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-15N HSQC
1313D 1H-15N NOESY
1413D HNHA
1513D HNHB
1622D 1H-13C HSQC
1742D 1H-13C HSQC
1823D HNCO
1923D HCACO
11023D HN(CO)CA
11123D HNCA
11223D CBCA(CO)NH
11323D HN(CA)CB
11423D C(CO)NH
11523D H(CCO)NH
11623D HBHA(CO)NH
11723D (H)CCH-TOCSY
11833D (H)CCH-TOCSY
11923D 1H-13C NOESY
12033D 1H-13C NOESY
12122D (HB)CB(CGCD)HD
12222D (HB)CB(CGCDCE)HE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.25-1.6 mM [U-15N] Jmj-ARID(615-730)-1, 90% H2O/10% D2O90% H2O/10% D2O
20.25-1.6 mM [U-13C; U-15N] Jmj-ARID(615-730)-2, 90% H2O/10% D2O90% H2O/10% D2O
30.25-1.6 mM [U-13C; U-15N] Jmj-ARID(615-730)-3, 100% D2O100% D2O
40.25-1.6 mM [U-10% 13C; U-15N] Jmj-ARID(615-730)-4, 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMJmj-ARID(615-730)-1[U-15N]0.25-1.61
mMJmj-ARID(615-730)-2[U-13C; U-15N]0.25-1.62
mMJmj-ARID(615-730)-3[U-13C; U-15N]0.25-1.63
mMJmj-ARID(615-730)-4[U-10% 13C; U-15N]0.25-1.64
Sample conditionsIonic strength: 90 / pH: 6.4 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker Avance IIBrukerAVANCE II7002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichcollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
PIPPGarrettdata analysis
RefinementMethod: simulated annealing / 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 / Representative conformer: 1

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