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- PDB-1ssf: Solution structure of the mouse 53BP1 fragment (residues 1463-1617) -

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Basic information

Entry
Database: PDB / ID: 1ssf
TitleSolution structure of the mouse 53BP1 fragment (residues 1463-1617)
ComponentsTransformation related protein 53 binding protein 1
KeywordsCELL CYCLE / Tudor domains / tandem / SH3-like fold / Beta barrel / alpha-helix
Function / homology
Function and homology information


chromosome, telomeric region => GO:0000781 / SUMOylation of transcription factors / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / kinetochore => GO:0000776 / G2/M DNA damage checkpoint / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / ubiquitin-modified histone reader activity / positive regulation of isotype switching ...chromosome, telomeric region => GO:0000781 / SUMOylation of transcription factors / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / kinetochore => GO:0000776 / G2/M DNA damage checkpoint / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / DNA repair complex / telomeric DNA binding / transcription factor binding / negative regulation of double-strand break repair via homologous recombination / methylated histone binding / DNA damage checkpoint signaling / replication fork / transcription coregulator activity / protein homooligomerization / kinetochore / double-strand break repair via nonhomologous end joining / p53 binding / site of double-strand break / histone binding / sequence-specific DNA binding / damaged DNA binding / nuclear body / DNA repair / DNA damage response / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / SH3 type barrels. - #30 / SH3 type barrels. - #140 / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / SH3 type barrels. / Ribosomal protein L2, domain 2 ...Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / SH3 type barrels. - #30 / SH3 type barrels. - #140 / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / SH3 type barrels. / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
TP53-binding protein 1 / TP53-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsCharier, G. / Couprie, J. / Alpha-Bazin, B. / Meyer, V. / Quemeneur, E. / Guerois, R. / Callebaut, I. / Gilquin, B. / Zinn-Justin, S.
CitationJournal: Structure / Year: 2004
Title: The Tudor Tandem of 53BP1; A New Structural Motif Involved in DNA and RG-Rich Peptide Binding
Authors: Charier, G. / Couprie, J. / Alpha-Bazin, B. / Meyer, V. / Quemeneur, E. / Guerois, R. / Callebaut, I. / Gilquin, B. / Zinn-Justin, S.
History
DepositionMar 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 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: 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
A: Transformation related protein 53 binding protein 1


Theoretical massNumber of molelcules
Total (without water)17,4271
Polymers17,4271
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 / 1000back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy conformer

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Components

#1: Protein Transformation related protein 53 binding protein 1 / murine p53-binding protein


Mass: 17426.572 Da / Num. of mol.: 1 / Fragment: Residues 1463-1617
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: Q91YC9, UniProt: P70399*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1333D 13C-separated NOESY
1423D 13C NOESY aromatic
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM mouse 53BP1 (1463-1617) fragment, U-15N, 50mM Tris-HCl buffer, 150mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
20.9mM mouse 53BP1 (1463-1617) fragment, U-15N,13C, 50mM Tris-HCl buffer, 150mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
30.9mM mouse 53BP1 (1463-1617) fragment, U-15N,13C, 50mM Tris-HCl buffer, 150mM NaCl, 100% D2O100% D2O
Sample conditionsIonic strength: 50mM Tris-Hcl, 150mM NaCl / pH: 7.2 / Pressure: ambient / Temperature: 300 K

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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 DRXBrukerDRX7501
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionClassification
XwinNMR2.5collection
NMRPipe2processing
Felix2000.1data analysis
CNS1refinement
CNS1structure solution
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 2337 NOE-derived restraints, 206 dihedral angle restraints, and 60 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy conformer
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the ...Conformer selection criteria: back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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