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- PDB-5agq: Solution structure of the TAM domain of human TIP5 BAZ2A involved... -

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Basic information

Entry
Database: PDB / ID: 5agq
TitleSolution structure of the TAM domain of human TIP5 BAZ2A involved in epigenetic regulation of rRNA genes
ComponentsBROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2A
KeywordsTRANSCRIPTION / TAM DOMAIN / TIP5/BAZ2A / PROTEIN RNA INTERACTION / EPIGENETICS / RRNA GENE SILENCING
Function / homology
Function and homology information


NoRC complex / : / : / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / : / negative regulation of transcription by RNA polymerase I / : ...NoRC complex / : / : / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / : / negative regulation of transcription by RNA polymerase I / : / heterochromatin formation / nuclear receptor binding / lysine-acetylated histone binding / NoRC negatively regulates rRNA expression / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / nucleolus / regulation of DNA-templated transcription / DNA binding / RNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif ...Bromodomain adjacent to zinc finger domain protein 2A / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / BAZ2A/BAZ2B, bromodomain / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Methyl-CpG binding domain / Methyl-CpG DNA binding / Methyl-CpG binding domain / Methyl-CpG-binding domain (MBD) profile. / DNA-binding domain superfamily / PHD-finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Bromodomain adjacent to zinc finger domain protein 2A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / ARIA2, CNS
AuthorsAnosova, I. / Melnik, S. / Tripsianes, K. / Kateb, F. / Grummt, I. / Sattler, M.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: A Novel RNA Binding Surface of the Tam Domain of Tip5/Baz2A Mediates Epigenetic Regulation of Rrna Genes.
Authors: Anosova, I. / Melnik, S. / Tripsianes, K. / Kateb, F. / Grummt, I. / Sattler, M.
History
DepositionFeb 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2A


Theoretical massNumber of molelcules
Total (without water)13,4171
Polymers13,4171
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200BEST ENERGY
RepresentativeModel #1

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Components

#1: Protein BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2A / TRANSCRIPTION TERMINATION FACTOR I-INTERACTING PROTEIN 5 / TTF-I-INTERACTING PROTEIN 5 / TIP5 / ...TRANSCRIPTION TERMINATION FACTOR I-INTERACTING PROTEIN 5 / TTF-I-INTERACTING PROTEIN 5 / TIP5 / HWALP3 / HUMAN TIP5 BAZ2A


Mass: 13417.299 Da / Num. of mol.: 1 / Fragment: TAM DOMAIN, RESIDUES 543-650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UIF9
Sequence detailsRESIDUE NUMBERING ACCORDING TO ISOFORM 1. N-TERMINAL RESIDUES GLY-ALA-MET-GLU ARE ADDED BY CLONING ...RESIDUE NUMBERING ACCORDING TO ISOFORM 1. N-TERMINAL RESIDUES GLY-ALA-MET-GLU ARE ADDED BY CLONING AND REMAIN AFTER EXPRESSION TAG REMOVAL WITH TOBACCO ETCH VIRUS (TEV) PROTEASE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-HSQC
12113C-HSQC
131HN(CA)CB
141HN(CO)CACB
151CC(CO)NH- TOCSY
161(H)CCH-TOCSY
17115N- EDITED 3D NOESY
18113C- EDITED 3D NOESY (ALIPHATICS)
19113C-EDITED 3D NOESY (AROMATICS)
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED TIP5-TAM DOMAIN. THE SOLUTION STRUCTURE WAS DEFINED BASED ON 2732 DISTANCE RESTRAINTS, DERIVED FROM ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED TIP5-TAM DOMAIN. THE SOLUTION STRUCTURE WAS DEFINED BASED ON 2732 DISTANCE RESTRAINTS, DERIVED FROM CYANA 3.0, TORSION ANGLE RESTRAINTS AND TWO SETS OF RDCS FROM TWO DIFFERENT ALIGNMENT MEDIA. VALIDATION PERFORMED WITH ICING WEB, PROCHECK AND WHATCHECK.

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Sample preparation

DetailsContents: 20MM SODIUM PHOSPHATE PH 7. 0, 50MM NACL, 1MM DTT, 90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM / pH: 7.0 / Pressure: 1.0 atm / Temperature: 293.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE, JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON, WARRENrefinement
Sparkystructure solution
CYANA3structure solution
RefinementMethod: ARIA2, CNS / Software ordinal: 1
NMR ensembleConformer selection criteria: BEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 20

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