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- PDB-2mam: Solution structure of the interdigitated double Tudor domain of RBBP1 -

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Basic information

Entry
Database: PDB / ID: 2mam
TitleSolution structure of the interdigitated double Tudor domain of RBBP1
ComponentsAT-rich interactive domain-containing protein 4A
KeywordsDNA BINDING PROTEIN / Retinoblastoma binding protein 1 / interdigitated double Tudor domain
Function / homology
Function and homology information


establishment of Sertoli cell barrier / : / genomic imprinting / negative regulation of stem cell population maintenance / positive regulation of stem cell population maintenance / erythrocyte development / transcription repressor complex / negative regulation of cell migration / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway ...establishment of Sertoli cell barrier / : / genomic imprinting / negative regulation of stem cell population maintenance / positive regulation of stem cell population maintenance / erythrocyte development / transcription repressor complex / negative regulation of cell migration / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / spermatogenesis / Potential therapeutics for SARS / transcription by RNA polymerase II / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
: / : / RBB1NT / RBB1NT (NUC162) domain / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain ...: / : / RBB1NT / RBB1NT (NUC162) domain / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / 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 / Tudor domain / Tudor domain / SH3 type barrels. - #140 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsGong, W. / Feng, Y.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Retinoblastoma-binding protein 1 has an interdigitated double Tudor domain with DNA binding activity.
Authors: Gong, W. / Wang, J. / Perrett, S. / Feng, Y.
History
DepositionJul 15, 2013Deposition site: BMRB / Processing site: PDBJ
SupersessionJan 15, 2014ID: 2LCD
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AT-rich interactive domain-containing protein 4A


Theoretical massNumber of molelcules
Total (without water)13,1731
Polymers13,1731
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 #1minimized average structure

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Components

#1: Protein AT-rich interactive domain-containing protein 4A / ARID domain-containing protein 4A / Retinoblastoma-binding protein 1 / RBBP-1


Mass: 13172.862 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 4-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID4A, RBBP1, RBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29374

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HNCO
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D HCACO
11013D (H)CCH-COSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY aliphatic
1131CCH-TOCSY

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Sample preparation

DetailsContents: 0.6 mM [U-95% 13C; U-95% 15N] entity-1, 10 % [U-99% 2H] D2O-2, 0.0004 % DSS-3, 15 mM DTT-4, 50 mM sodium chloride-5, 50 mM TRIS-6, 2 mM EDTA-7, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMentity-1[U-95% 13C; U-95% 15N]1
10 %D2O-2[U-99% 2H]1
0.0004 %DSS-31
15 mMDTT-41
50 mMsodium chloride-51
50 mMTRIS-61
2 mMEDTA-71
Sample conditionsIonic strength: 100 / pH: 7.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipe9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
cns1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1 / Details: water refine
NMR representativeSelection criteria: minimized average structure
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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