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- PDB-2oeh: Determination of the Three-dimensional Structure of the Mrf2-DNA ... -

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Basic information

Entry
Database: PDB / ID: 2oeh
TitleDetermination of the Three-dimensional Structure of the Mrf2-DNA Complex Using Paramagnetic Spin Labeling
Components
  • 5'-D(P*CP*GP*AP*CP*GP*TP*TP*AP*TP*AP*TP*TP*GP*T)-3'
  • 5'-D(P*TP*AP*CP*AP*AP*TP*AP*TP*AP*AP*CP*GP*TP*CP*G)-3'
  • AT-rich interactive domain-containing protein 5B
KeywordsTranscription/DNA / Mrf2 / DNA / complex / spin labeling / Transcription-DNA COMPLEX
Function / homology
Function and homology information


muscle organ morphogenesis / cell development / fibroblast migration / face morphogenesis / fat pad development / skeletal system morphogenesis / adrenal gland development / female gonad development / fat cell differentiation / platelet-derived growth factor receptor signaling pathway ...muscle organ morphogenesis / cell development / fibroblast migration / face morphogenesis / fat pad development / skeletal system morphogenesis / adrenal gland development / female gonad development / fat cell differentiation / platelet-derived growth factor receptor signaling pathway / roof of mouth development / adipose tissue development / positive regulation of DNA-binding transcription factor activity / cellular response to leukemia inhibitory factor / post-embryonic development / kidney development / liver development / HDMs demethylate histones / multicellular organism growth / male gonad development / transcription coactivator activity / 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 / DNA binding / nucleoplasm / nucleus
Similarity search - Function
AT-rich interactive domain-containing protein 5B / ARID 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 / ARID/BRIGHT DNA binding domain / DNA polymerase; domain 1 ...AT-rich interactive domain-containing protein 5B / ARID 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 / ARID/BRIGHT DNA binding domain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / AT-rich interactive domain-containing protein 5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsCai, S. / Zhu, L. / Zhang, Z.
CitationJournal: Biochemistry / Year: 2007
Title: Determination of the three-dimensional structure of the Mrf2-DNA complex using paramagnetic spin labeling.
Authors: Cai, S. / Zhu, L. / Zhang, Z. / Chen, Y.
History
DepositionDec 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(P*TP*AP*CP*AP*AP*TP*AP*TP*AP*AP*CP*GP*TP*CP*G)-3'
C: 5'-D(P*CP*GP*AP*CP*GP*TP*TP*AP*TP*AP*TP*TP*GP*T)-3'
A: AT-rich interactive domain-containing protein 5B


Theoretical massNumber of molelcules
Total (without water)21,5153
Polymers21,5153
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(P*TP*AP*CP*AP*AP*TP*AP*TP*AP*AP*CP*GP*TP*CP*G)-3'


Mass: 4577.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase synthesis
#2: DNA chain 5'-D(P*CP*GP*AP*CP*GP*TP*TP*AP*TP*AP*TP*TP*GP*T)-3'


Mass: 4285.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase synthesis
#3: Protein AT-rich interactive domain-containing protein 5B / ARID domain- containing protein 5B / Mrf1-like / Modulator recognition factor 2 / MRF-2


Mass: 12652.646 Da / Num. of mol.: 1 / Fragment: ARID domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID5B, DESRT, MRF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14865

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D HSQC

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Sample preparation

DetailsContents: 0.5mM Mrf-2 ARID domain, U-15N; 10mM phosphate buffer; 90% H2O, 10% D2O; pH=6
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
HADDOCKBonvin, A. M. J. J.structure solution
HADDOCKBonvin, A. M. J. J.refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: 13 distance constraints from spin labeling; the majority of the protein and DNA are fixed
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 17

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