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- PDB-2rp4: Solution Structure of the oligomerization domain in Dmp53 -

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Basic information

Entry
Database: PDB / ID: 2rp4
TitleSolution Structure of the oligomerization domain in Dmp53
ComponentsTranscription factor p53
KeywordsTRANSCRIPTION / Dmp53 / p53 / oligomerization domain / tetramerizaiton domain / Nucleus
Function / homology
Function and homology information


positive regulation of cellular response to X-ray / positive regulation of growth rate / negative regulation of insulin-like growth factor receptor signaling pathway / negative regulation of photoreceptor cell differentiation / regulation of apoptosis involved in tissue homeostasis / neuroblast differentiation / TFIIH-class transcription factor complex binding / tissue regeneration / regulation of organ growth / positive regulation of multicellular organism growth ...positive regulation of cellular response to X-ray / positive regulation of growth rate / negative regulation of insulin-like growth factor receptor signaling pathway / negative regulation of photoreceptor cell differentiation / regulation of apoptosis involved in tissue homeostasis / neuroblast differentiation / TFIIH-class transcription factor complex binding / tissue regeneration / regulation of organ growth / positive regulation of multicellular organism growth / reciprocal meiotic recombination / ubiquitin conjugating enzyme binding / RNA polymerase II general transcription initiation factor binding / oogenesis / response to ionizing radiation / positive regulation of macroautophagy / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ectopic germ cell programmed cell death / regulation of DNA repair / response to UV / positive regulation of cell cycle / cellular response to starvation / DNA damage response, signal transduction by p53 class mediator / determination of adult lifespan / response to radiation / positive regulation of protein import into nucleus / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of cell population proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process / ubiquitin protein ligase binding / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus
Similarity search - Function
Transcription factor p53, C-terminal domain / Transcription factor p53, C-terminal, Drosophila / Drosophila transcription factor p53, C-terminal domain superfamily / Transcription factor P53 - C terminal domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding ...Transcription factor p53, C-terminal domain / Transcription factor p53, C-terminal, Drosophila / Drosophila transcription factor p53, C-terminal domain superfamily / Transcription factor P53 - C terminal domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsOu, H.D. / Doetsch, V.
CitationJournal: Embo J. / Year: 2007
Title: Structural evolution of C-terminal domains in the p53 family
Authors: Ou, H.D. / Loehr, F. / Vogel, V. / Maentele, W. / Doetsch, V.
History
DepositionApr 30, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor p53
B: Transcription factor p53
C: Transcription factor p53
D: Transcription factor p53


Theoretical massNumber of molelcules
Total (without water)34,2914
Polymers34,2914
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein
Transcription factor p53 / GH11591p / Transcription factor / P53 tumor suppressor-like protein / P53-like regulator of ...GH11591p / Transcription factor / P53 tumor suppressor-like protein / P53-like regulator of apoptosis and cell cycle / CG33336-PA / isoform A


Mass: 8572.663 Da / Num. of mol.: 4
Fragment: Oligomerization domain of the Dmp53, UNP residues 315-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: p53, prac, CG10873, Dmel_CG33336 / Plasmid: pBH4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9N6D8, UniProt: Q8IH92*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCA
1313D 1H-15N NOESY
1423D 1H-13C NOESY
1532D 1H-1H NOESY
1644D J Resolved NOESY
1732D 1H-1H TOCSY
1823D HN(CO)CA

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Sample preparation

Details
Solution-IDContentsSolvent system
120mM sodium phosphate, 100mM sodium chloride, 0.03% sodium azide, 0.5-0.8mM [U-15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
220mM sodium phosphate, 100mM sodium chloride, 0.03% sodium azide, 0.5-0.8mM [U-13C; U-15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
320mM sodium phosphate, 100mM sodium chloride, 0.5-0.8mM protein, 100% D2O100% D2O
420mM sodium phosphate, 100mM sodium chloride, 0.5mM [U-13C; U-15N] protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphate1
100 mMsodium chloride1
0.03 %sodium azide1
0.5 mMprotein[U-15N]1
20 mMsodium phosphate2
100 mMsodium chloride2
0.03 %sodium azide2
0.5 mMprotein[U-13C; U-15N]2
20 mMsodium phosphate3
100 mMsodium chloride3
0.5 mMprotein3
20 mMsodium phosphate4
100 mMsodium chloride4
0.5 mMprotein[U-13C; U-15N]4
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue, Nilgeschemical shift assignment
ARIA1.2Linge, O'Donoghue, Nilgesrefinement
XEASYBartels et al.chemical shift assignment
TALOSCornilescu, Delaglio, Baxgeometry optimization
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 100 structures were calculated with Aria1.2, then 20 lowest energies structures underwent water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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