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- PDB-7dm4: Solution structure of ARID4B Tudor domain -

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Basic information

Entry
Database: PDB / ID: 7dm4
TitleSolution structure of ARID4B Tudor domain
ComponentsAT-rich interactive domain-containing protein 4B
KeywordsDNA BINDING PROTEIN / ARID4B / interdigitated / Tudor / disorder region
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 / Sin3-type complex / negative regulation of cell migration / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / NoRC negatively regulates rRNA expression / spermatogenesis ...establishment of Sertoli cell barrier / genomic imprinting / negative regulation of stem cell population maintenance / positive regulation of stem cell population maintenance / Sin3-type complex / negative regulation of cell migration / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / NoRC negatively regulates rRNA expression / spermatogenesis / Potential therapeutics for SARS / transcription by RNA polymerase II / transcription cis-regulatory region binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
AT-rich interactive domain-containing protein 4B / : / : / RBB1NT / RBB1NT (NUC162) domain / : / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / ARID DNA-binding domain / ARID DNA-binding domain superfamily ...AT-rich interactive domain-containing protein 4B / : / : / RBB1NT / RBB1NT (NUC162) domain / : / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / 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 / ARID/BRIGHT DNA binding domain / Tudor domain / Tudor domain / Chromo-like domain superfamily
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsRen, J. / Yao, H. / Hu, W. / Perrett, S. / Feng, Y. / Gong, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31470747 China
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis for the DNA-binding activity of human ARID4B Tudor domain.
Authors: Ren, J. / Yao, H. / Hu, W. / Perrett, S. / Gong, W. / Feng, Y.
History
DepositionDec 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jun 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 1.4May 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,9101
Polymers16,9101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11920 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein AT-rich interactive domain-containing protein 4B


Mass: 16910.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID4B, BRCAA1, RBBP1L1, RBP1L1, SAP180 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4LE39

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CA)CB
191isotropic13D HN(CA)CO
181isotropic13D CBCA(CO)NH
171isotropic13D (H)CCH-TOCSY
161isotropic13D CCH-TOCSY
1141isotropic13D HBHA(CO)NH
1101isotropic13D C(CO)NH
1111isotropic23D 1H-15N NOESY
1121isotropic23D 1H-13C NOESY aliphatic
1131isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.6 mM [U-13C; U-15N] ARID4B Tudor domain, 2 mM DTT, 2 mM EDTA, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O
Label: 15N, 13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMARID4B Tudor domain[U-13C; U-15N]1
2 mMDTTnatural abundance1
2 mMEDTAnatural abundance1
100 mMsodium chloridenatural abundance1
20 mMsodium phosphatenatural abundance1
Sample conditionsIonic strength: 0.14 M / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 302 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJJohnson, One Moon Scientificchemical shift assignment
NMRViewJJohnson, One Moon Scientificpeak picking
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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