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- PDB-1kqq: Solution Structure of the Dead ringer ARID-DNA Complex -

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Basic information

Entry
Database: PDB / ID: 1kqq
TitleSolution Structure of the Dead ringer ARID-DNA Complex
Components
  • 5'-D(*CP*CP*AP*CP*AP*TP*CP*AP*AP*TP*AP*CP*AP*GP*G)-3'
  • 5'-D(*CP*CP*TP*GP*TP*AP*TP*TP*GP*AP*TP*GP*TP*GP*G)-3'
  • DEAD RINGER PROTEIN
KeywordsTRANSCRIPTION/DNA / ARID / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of female receptivity / salivary gland development / male courtship behavior / embryonic pattern specification / gliogenesis / dendrite morphogenesis / muscle organ development / anterior/posterior pattern specification / oogenesis / axon guidance ...regulation of female receptivity / salivary gland development / male courtship behavior / embryonic pattern specification / gliogenesis / dendrite morphogenesis / muscle organ development / anterior/posterior pattern specification / oogenesis / axon guidance / DNA-binding transcription factor binding / transcription cis-regulatory region binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
REKLES domain / AT-rich interactive domain-containing protein 3 / REKLES domain profile. / ARID DNA-binding domain / 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 ...REKLES domain / AT-rich interactive domain-containing protein 3 / REKLES domain profile. / ARID DNA-binding domain / 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 / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein dead ringer
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsIwahara, J. / Iwahara, M. / Daughdrill, G.W. / Ford, J. / Clubb, R.T.
CitationJournal: EMBO J. / Year: 2002
Title: The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA.
Authors: Iwahara, J. / Iwahara, M. / Daughdrill, G.W. / Ford, J. / Clubb, R.T.
History
DepositionJan 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: 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(*CP*CP*TP*GP*TP*AP*TP*TP*GP*AP*TP*GP*TP*GP*G)-3'
C: 5'-D(*CP*CP*AP*CP*AP*TP*CP*AP*AP*TP*AP*CP*AP*GP*G)-3'
A: DEAD RINGER PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,3243
Polymers25,3243
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 4631.005 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*AP*CP*AP*TP*CP*AP*AP*TP*AP*CP*AP*GP*G)-3'


Mass: 4546.990 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DEAD RINGER PROTEIN


Mass: 16145.514 Da / Num. of mol.: 1 / Fragment: A/T Rich Interaction Domain / Mutation: F355L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dri / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q24573

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
1423D 13C-separated NOESY
1522D F1F2 13C-filtered NOESY
1613D F1 13C15N-filtered F2 13C-edited NOESY
1713D F1 13C15N-filtered F2 15N-edited NOESY
1822D F2 13C-filtered NOESY
1922D F1 13C-filtered JUNSY
11013D HNHB
NMR detailsText: The structure was determined using triple-resonance NMR methods along with various isotope-filtered techniques. Residues 1-2 and 134-139 are disordered in solution.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.0mM Dead ringer-DNA complex (protein U-13C,15N, DNA NA) 20mM Tris U-2H, 0.01% NaN3 NA, 0.5mM EDTA NA, 5mM DTT U-2H93% H2O/7% D2O
21.4mM Dead ringer-DNA complex (protein U-13C,15N, DNA NA) 20mM Tris U-2H, 0.01% NaN3 NA, 0.5mM EDTA NA, 5mM DTT U-2H100% D2O
Sample conditionsIonic strength: 0 / pH: 6.7 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Varian UNITYPLUSVarianUNITYPLUS7503

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2Delaglioprocessing
NMRView4.3Johnsondata analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 3402 restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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