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- PDB-1q1v: Structure of the Oncoprotein DEK: a putative DNA-binding Domain R... -

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Basic information

Entry
Database: PDB / ID: 1q1v
TitleStructure of the Oncoprotein DEK: a putative DNA-binding Domain Related to the Winged Helix Motif
ComponentsDEK protein
KeywordsDNA BINDING PROTEIN / WINGED-HELIX MOTIF
Function / homology
Function and homology information


Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / regulation of double-strand break repair via nonhomologous end joining / contractile muscle fiber / 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 by the AP-2 (TFAP2) family of transcription factors / regulation of double-strand break repair via nonhomologous end joining / contractile muscle fiber / 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 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDevany, M. / Kotharu, N.P. / Matsuo, H.
CitationJournal: PROTEIN SCI. / Year: 2004
Title: Solution NMR structure of the C-terminal domain of the human protein DEK
Authors: Devany, M. / Kotharu, N.P. / Matsuo, H.
History
DepositionJul 22, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEK protein


Theoretical massNumber of molelcules
Total (without water)8,2661
Polymers8,2661
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)10 / 80STRUCTURES WITH THE LOWEST TOTAL ENERGY
RepresentativeModel #1

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Components

#1: Protein DEK protein


Mass: 8265.648 Da / Num. of mol.: 1 / Fragment: RESIDUES 309-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: dek / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / 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
1313D (H)CCH-TOCSY
NMR detailsText: DISTANCE RESTRAINTS COLLECTED FROM A NOESY SPECTRUM WITH 150MS MIXING TIME.

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Sample preparation

DetailsContents: 1.0MM DEK C-TERMINAL DOMAIN
Sample conditionsIonic strength: 50mM NAPO4, 100mM KCL / pH: 6.75 / Pressure: AMBIENT / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURE BASED ON 1456 NON-REDUNDANT NOES, 33 HYDROGEN BOND RESTRAINTS DERIVED FROM DEUTERIUM EXCHANG EXPERIMENTS, AND 46 DIHEDRAL-ANGLE RESTRAINTS DERIVED FROM CA CHEMICAL SHIFTS.
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LOWEST TOTAL ENERGY
Conformers calculated total number: 80 / Conformers submitted total number: 10

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