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- PDB-2jv0: SET domain of RIZ1 tumor suppressor (PRDM2) -

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Basic information

Entry
Database: PDB / ID: 2jv0
TitleSET domain of RIZ1 tumor suppressor (PRDM2)
ComponentsPR domain zinc finger protein 2
KeywordsTRANSCRIPTION / SET domain / PR domain / RIZ1 / PRDM2 / protein lysine methyltransferase / histone lysine methyltransferase / HKMT / Activator / Alternative initiation / DNA-binding / Metal-binding / Nucleus / Phosphorylation / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


[histone H3]-lysine9 N-trimethyltransferase / histone H3K9 trimethyltransferase activity / determination of adult lifespan / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / methylation / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity ...[histone H3]-lysine9 N-trimethyltransferase / histone H3K9 trimethyltransferase activity / determination of adult lifespan / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / methylation / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / Golgi apparatus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
PR domain zinc finger protein 2 / PRDM2, PR/SET domain / PR domain zinc finger protein 2, PR domain / C2H2-type zinc finger / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / Zinc finger, C2H2 type ...PR domain zinc finger protein 2 / PRDM2, PR/SET domain / PR domain zinc finger protein 2, PR domain / C2H2-type zinc finger / Beta-clip-like / SET domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / Zinc finger, C2H2 type / SET domain profile. / SET domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Beta Complex / Mainly Beta
Similarity search - Domain/homology
PR domain zinc finger protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBriknarova, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Structural studies of the SET domain from RIZ1 tumor suppressor
Authors: Briknarova, K. / Zhou, X. / Satterthwait, A. / Hoyt, D.W. / Ely, K.R. / Huang, S.
History
DepositionSep 10, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.3Oct 20, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_validate_polymer_linkage / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PR domain zinc finger protein 2


Theoretical massNumber of molelcules
Total (without water)18,5251
Polymers18,5251
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)16 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PR domain zinc finger protein 2 / PR domain-containing protein 2 / Retinoblastoma protein-interacting zinc finger protein / Zinc ...PR domain-containing protein 2 / Retinoblastoma protein-interacting zinc finger protein / Zinc finger protein RIZ / MTE-binding protein / MTB-ZF / GATA-3-binding protein G3B


Mass: 18524.959 Da / Num. of mol.: 1 / Fragment: SET domain residues 1-161 / Mutation: N2D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDM2, RIZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q13029

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY
1323D 1H-13C aromatic NOESY
1444D 15N,15N NOESY
1533D CBCA(CO)NH
1633D C(CO)NH
1733D HN(CA)CB
1823D H(CCO)NH
1923D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4-1 mM [U-99% 15N] entity_1, 20 mM potassium phosphate, 50 mM potassium chloride, 2.5 mM DTT, 0-2 mM EDTA, 0-4.5 mM S-adenosyl-L-homocysteine, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-99% 13C; U-99% 15N] entity_1, 20 mM potassium phosphate, 50 mM potassium chloride, 2.5 mM DTT, 0-2 mM EDTA, 0-4.5 mM S-adenosyl-L-homocysteine, 90% H2O/10% D2O90% H2O/10% D2O
30.5-1 mM [U-99% 13C; U-99% 15N; 80% 2H] entity_1, 20 mM potassium phosphate, 50 mM potassium chloride, 2.5 mM DTT, 1-2 mM EDTA, 0-4.5 mM S-adenosyl-L-homocysteine, 90% H2O/10% D2O90% H2O/10% D2O
40.9 mM [U-99% 15N; 80% 2H] entity_1, 20 mM potassium phosphate, 50 mM potassium chloride, 2.5 mM DTT, 1-2 mM EDTA, 4.5 mM S-adenosyl-L-homocysteine, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1[U-99% 15N]0.4-11
20 mMpotassium phosphate1
50 mMpotassium chloride1
2.5 mMDTT1
mMEDTA0-21
mMS-adenosyl-L-homocysteine0-4.51
0.8 mMentity_1[U-99% 13C; U-99% 15N]2
20 mMpotassium phosphate2
50 mMpotassium chloride2
2.5 mMDTT2
mMEDTA0-22
mMS-adenosyl-L-homocysteine0-4.52
mMentity_1[U-99% 13C; U-99% 15N; 80% 2H]0.5-13
20 mMpotassium phosphate3
50 mMpotassium chloride3
2.5 mMDTT3
mMEDTA1-23
mMS-adenosyl-L-homocysteine0-4.53
0.9 mMentity_1[U-99% 15N; 80% 2H]4
20 mMpotassium phosphate4
50 mMpotassium chloride4
2.5 mMDTT4
mMEDTA1-24
4.5 mMS-adenosyl-L-homocysteine4
Sample conditionsIonic strength: 0.082 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.data analysis
FelixAccelrys Software Inc.processing
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
X-PLOR NIH2.13Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 16

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