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- PDB-2jx3: NMR solution structure of the N-terminal domain of DEK -

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Basic information

Entry
Database: PDB / ID: 2jx3
TitleNMR solution structure of the N-terminal domain of DEK
ComponentsProtein DEK
KeywordsDNA BINDING PROTEIN / alpha helix / SAF/SAP motif / DNA binding / Chromosomal rearrangement / DNA-binding / Nucleus / Phosphorylation / Proto-oncogene
Function / homology
Function and homology information


regulation of double-strand break repair via nonhomologous end joining / contractile muscle fiber / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / B-WICH complex / regulation of double-strand break repair / positive regulation of transcription by RNA polymerase III / positive regulation of transcription by RNA polymerase I / viral genome replication / B-WICH complex positively regulates rRNA expression / Transcriptional regulation of granulopoiesis ...regulation of double-strand break repair via nonhomologous end joining / contractile muscle fiber / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / B-WICH complex / regulation of double-strand break repair / positive regulation of transcription by RNA polymerase III / positive regulation of transcription by RNA polymerase I / viral genome replication / B-WICH complex positively regulates rRNA expression / Transcriptional regulation of granulopoiesis / histone binding / transcription by RNA polymerase II / chromatin remodeling / nucleolus / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
Protein DEK / DEK C-terminal (DEK-C) domain profile. / DEK, C-terminal / DEK C terminal domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMatsuo, H. / Devany, M.
CitationJournal: Protein Sci. / Year: 2008
Title: Solution NMR structure of the N-terminal domain of the human DEK protein
Authors: Devany, M. / Kappes, F. / Chen, K.M. / Markovitz, D.M. / Matsuo, H.
History
DepositionNov 2, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: 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 1.3May 29, 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
A: Protein DEK


Theoretical massNumber of molelcules
Total (without water)15,1041
Polymers15,1041
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)10 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein DEK


Mass: 15103.931 Da / Num. of mol.: 1 / Fragment: SAP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35659

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.65 mM [U-100% 13C; U-100% 15N] DEK78-208, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.65 mM / Component: DEK78-208 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100mM KCL / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: initial temp=2000, cooling steps= 60000
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 10

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