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- PDB-2mw4: Tetramerization domain of the Ciona intestinalis p53/p73-b transc... -

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Basic information

Entry
Database: PDB / ID: 2mw4
TitleTetramerization domain of the Ciona intestinalis p53/p73-b transcription factor protein
ComponentsTranscription factor protein
KeywordsTRANSCRIPTION / Ciona intestinalis / p53/p73-b / transcription factor / tetramerization domain
Function / homology
Function and homology information


protein tetramerization / transcription cis-regulatory region binding / DNA-binding transcription factor activity / apoptotic process / metal ion binding / nucleus
Similarity search - Function
p53, subunit A / p53-like tetramerisation domain / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding ...p53, subunit A / p53-like tetramerisation domain / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Uncharacterized protein / Transcription factor protein
Similarity search - Component
Biological speciesCiona intestinalis (vase tunicate)
MethodSOLUTION NMR / simulated annealing, energy minimization
AuthorsHeering, J.P. / Jonker, H.R.A. / Loehr, F. / Schwalbe, H. / Doetsch, V.
CitationJournal: Protein Sci. / Year: 2016
Title: Structural investigations of the p53/p73 homologs from the tunicate species Ciona intestinalis reveal the sequence requirements for the formation of a tetramerization domain.
Authors: Heering, J. / Jonker, H.R. / Lohr, F. / Schwalbe, H. / Dotsch, V.
History
DepositionOct 27, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,1134
Polymers22,1134
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide
Transcription factor protein /


Mass: 5528.365 Da / Num. of mol.: 4 / Fragment: Tetramerization domain (UNP residues 374-419)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Gene: Ci-p53/p73-b / Plasmid: pBH4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4H2Z8, UniProt: F6SSG7*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
1222D 1H-13C HSQC
1323D HN(CA)CB
1423D HNCO
1523D (H)CC(CO)NH
1623D CC(CO)NH
1723D (H)CCH-TOCSY
1823D 1H-13C NOESY aliphatic
1933D 1H-13C NOESY aromatic
11033D 1H-13C NOESY 15N-edited inter
11133D 1H-13C HMQC-NOESY-15N-1H-TROSY
11233D 1H-13C NOESY J-resolved
11313D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM [U-100% 15N] protein, 50 mM L-arginine, 50 mM L-glutamate, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
22.5 mM [U-100% 13C; U-100% 15N] protein, 50 mM L-arginine, 50 mM L-glutamate, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
32 mM [U-100% 15N] protein, 2 mM [U-100% 13C] protein, 50 mM L-arginine, 50 mM L-glutamate, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMentity-1[U-100% 15N]1
50 mML-arginine-21
50 mML-glutamate-31
1 mMDTT-41
2.5 mMentity-5[U-100% 13C; U-100% 15N]2
50 mML-arginine-62
50 mML-glutamate-72
1 mMDTT-82
2 mMentity-9[U-100% 15N]3
2 mMentity-10[U-100% 13C]3
50 mML-arginine-113
50 mML-glutamate-123
1 mMDTT-133
Sample conditionsIonic strength: 0 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004
Bruker AvanceBrukerAVANCE5005

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.9Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddarddata analysis
Sparky3.114Goddardpeak picking
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
Details: SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS, REFINEMENT IN EXPLICIT WATER
NMR constraintsNOE constraints total: 1433 / NOE intraresidue total count: 300 / NOE long range total count: 38 / NOE medium range total count: 293 / NOE sequential total count: 322 / Hydrogen bond constraints total count: 40
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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