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- PDB-2mwo: Solution structure of 53BP1 tandem Tudor domains in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2mwo
TitleSolution structure of 53BP1 tandem Tudor domains in complex with a p53K370me2 peptide
Components
  • Cellular tumor antigen p53
  • Tumor suppressor p53-binding protein 1
KeywordsTRANSCRIPTION/ANTITUMOR PROTEIN / Cell cycle / DNA damage response / TRANSCRIPTION-ANTITUMOR PROTEIN complex
Function / homology
Function and homology information


histone H4K20me methyltransferase activity / positive regulation of isotype switching / ubiquitin-modified histone reader activity / histone H4K20me2 reader activity / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator ...histone H4K20me methyltransferase activity / positive regulation of isotype switching / ubiquitin-modified histone reader activity / histone H4K20me2 reader activity / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / regulation of cell cycle G2/M phase transition / DNA repair complex / oligodendrocyte apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / circadian behavior / cellular response to actinomycin D / positive regulation of programmed necrotic cell death / histone deacetylase regulator activity / RUNX3 regulates CDKN1A transcription / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / Urea cycle / Regulation of TP53 Activity through Association with Co-factors / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / intrinsic apoptotic signaling pathway by p53 class mediator / entrainment of circadian clock by photoperiod / Zygotic genome activation (ZGA) / telomeric repeat DNA binding / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / hematopoietic progenitor cell differentiation / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Transcriptional Regulation by VENTX / replicative senescence / TFIID-class transcription factor complex binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / viral process / positive regulation of intrinsic apoptotic signaling pathway / Pyroptosis / determination of adult lifespan / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of fibroblast proliferation / general transcription initiation factor binding / positive regulation of execution phase of apoptosis / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / negative regulation of double-strand break repair via homologous recombination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cellular response to glucose starvation / core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / DNA damage checkpoint signaling / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / histone reader activity / transcription repressor complex / response to gamma radiation / tumor necrosis factor-mediated signaling pathway / 14-3-3 protein binding / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / molecular function activator activity / transcription initiation-coupled chromatin remodeling / Regulation of PTEN gene transcription / cellular response to ionizing radiation / cellular response to xenobiotic stimulus / DNA damage response, signal transduction by p53 class mediator / TP53 Regulates Metabolic Genes / double-strand break repair via nonhomologous end joining / TP53 Regulates Transcription of DNA Repair Genes / replication fork / Regulation of NF-kappa B signaling / mRNA 3'-UTR binding / protein tetramerization / autophagy / promoter-specific chromatin binding / Nonhomologous End-Joining (NHEJ) / Stabilization of p53 / molecular condensate scaffold activity / negative regulation of cell growth / cellular response to gamma radiation
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 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain ...Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / SH3 type barrels. - #30 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / SH3 type barrels. - #140 / : / p53 family signature. / 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 / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / SH3 type barrels. / Roll / Ribosomal protein L2, domain 2 / Mainly Beta
Similarity search - Domain/homology
Cellular tumor antigen p53 / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsCui, G. / Botuyan, M.V. / Mer, G.
CitationJournal: Structure / Year: 2015
Title: Structural Plasticity of Methyllysine Recognition by the Tandem Tudor Domain of 53BP1.
Authors: Tong, Q. / Cui, G. / Botuyan, M.V. / Rothbart, S.B. / Hayashi, R. / Musselman, C.A. / Singh, N. / Appella, E. / Strahl, B.D. / Mer, G. / Kutateladze, T.G.
History
DepositionNov 15, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif / struct_site
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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor suppressor p53-binding protein 1
B: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)15,6302
Polymers15,6302
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690.9 Å2
ΔGint-9.2 kcal/mol
Surface area2060 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Tumor suppressor p53-binding protein 1 / 53BP1 / p53-binding protein 1 / p53BP1


Mass: 13944.780 Da / Num. of mol.: 1 / Fragment: Tudor-like region residues 1484-1603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12888
#2: Protein/peptide Cellular tumor antigen p53 / p53K370Me2 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 1684.919 Da / Num. of mol.: 1 / Fragment: DNA-binding repression region residues 363-377 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04637
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-15N HSQC
1322D 1H-13C HSQC
1442D 1H-13C HSQC
1522D 1H-13C HSQC aromatic
1613D HNCA
1713D HN(CA)CB
1833D HN(CA)CB
1913D HNCO
11013D CBCA(CO)NH
11113D HN(CA)CO
11213D H(CCO)NH
11313D C(CO)NH
11413D HBHA(CO)NH
11513D (H)CCH-TOCSY
11652D 1H-15N HSQC
11753D 1H-15N TOCSY
11823D 1H-13C NOESY aliphatic
11923D 1H-13C NOESY aromatic
12053D 1H-15N NOESY
12123D 1H-15N NOESY
12223D Filtered (15N/13C)-Edited (13C)
12343D Filtered (15N/13C)-Edited (13C)
12423D (HB)CB(CGCD)HD
12562D 1H-13C HSQC
12672D 1H-13C HSQC
12772D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] 53BP1-Tudor, 6.0 mM p53K370me2, 90% H2O/10% D2O90% H2O/10% D2O
225 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] 53BP1-Tudor, 6.0 mM p53K370me2, 100% D2O100% D2O
325 mM sodium phosphate, 1.5 mM sodium azide, 5.0 mM 53BP1-Tudor, 2.0 mM [U-100% 13C; U-100% 15N] p53Kc370me2, 90% H2O/10% D2O90% H2O/10% D2O
425 mM sodium phosphate, 1.5 mM sodium azide, 5.0 mM 53BP1-Tudor, 2.0 mM [U-100% 13C; U-100% 15N] p53Kc370me2, 100% D2O100% D2O
525 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 15N] 53BP1-Tudor, 6.0 mM p53K370me2, 90% H2O/10% D2O90% H2O/10% D2O
635 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM p53K370me2, 100% D2O100% D2O
725 mM sodium phosphate, 1.5 mM sodium azide, 2.0 mM [U-100% 13C; U-100% 15N] p53Kc370me2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMsodium phosphate-11
1.5 mMsodium azide-21
2.0 mM53BP1-Tudor-3[U-100% 13C; U-100% 15N]1
6.0 mMp53K370me2-41
25 mMsodium phosphate-52
1.5 mMsodium azide-62
2.0 mM53BP1-Tudor-7[U-100% 13C; U-100% 15N]2
6.0 mMp53K370me2-82
25 mMsodium phosphate-93
1.5 mMsodium azide-103
5.0 mM53BP1-Tudor-113
2.0 mMp53Kc370me2-12[U-100% 13C; U-100% 15N]3
25 mMsodium phosphate-134
1.5 mMsodium azide-144
5.0 mM53BP1-Tudor-154
2.0 mMp53Kc370me2-16[U-100% 13C; U-100% 15N]4
25 mMsodium phosphate-175
1.5 mMsodium azide-185
2.0 mM53BP1-Tudor-19[U-100% 15N]5
6.0 mMp53K370me2-205
35 mMsodium phosphate-216
1.5 mMsodium azide-226
2.0 mMp53K370me2-236
25 mMsodium phosphate-247
1.5 mMsodium azide-257
2.0 mMp53Kc370me2-26[U-100% 13C; U-100% 15N]7
Sample conditionsIonic strength: 25 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificprocessing
SANEDuggan, Legge, Dyson & Wrightchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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