[English] 日本語
Yorodumi
- PDB-1ssf: Solution structure of the mouse 53BP1 fragment (residues 1463-1617) -

+
Open data


ID or keywords:

Loading...

-
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


SUMOylation of transcription factors / 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 / histone H4K20me2 reader activity / ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining ...SUMOylation of transcription factors / 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 / histone H4K20me2 reader activity / ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / negative regulation of double-strand break repair via homologous recombination / : / replication fork / transcription coregulator activity / protein homooligomerization / kinetochore / double-strand break repair via nonhomologous end joining / p53 binding / site of double-strand break / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA repair / DNA damage response / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / SH3 type barrels. - #30 / SH3 type barrels. - #140 / breast cancer carboxy-terminal domain / BRCT domain profile. ...Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more