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- PDB-2lvm: Solution structure of human 53BP1 tandem Tudor domains in complex... -

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Basic information

Entry
Database: PDB / ID: 2lvm
TitleSolution structure of human 53BP1 tandem Tudor domains in complex with a histone H4K20me2 peptide
Components
  • Histone H4
  • Tumor suppressor p53-binding protein 1
KeywordsCELL CYCLE / dimethylation
Function / homology
Function and homology information


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 / SUMOylation of transcription factors / negative regulation of megakaryocyte differentiation / negative regulation of double-strand break repair via homologous recombination ...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 / SUMOylation of transcription factors / negative regulation of megakaryocyte differentiation / negative regulation of double-strand break repair via homologous recombination / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / histone reader activity / Meiotic synapsis / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / DNA damage checkpoint signaling / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / transcription coregulator activity / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / protein homooligomerization / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / kinetochore / PKMTs methylate histone lysines / Meiotic recombination / positive regulation of DNA-binding transcription factor activity / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / double-strand break repair via nonhomologous end joining / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / p53 binding / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / site of double-strand break / HATs acetylate histones / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / chromosome, telomeric region / nuclear body / protein heterodimerization activity / Amyloid fiber formation / DNA damage response / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm
Similarity search - Function
: / BRCA1 C Terminus (BRCT) domain / 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. ...: / BRCA1 C Terminus (BRCT) domain / 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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / SH3 type barrels. / Histone-fold / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
Histone H4 / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsCui, G. / Botuyan, M. / Mer, G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Acetylation limits 53BP1 association with damaged chromatin to promote homologous recombination.
Authors: Tang, J. / Cho, N.W. / Cui, G. / Manion, E.M. / Shanbhag, N.M. / Botuyan, M.V. / Mer, G. / Greenberg, R.A.
History
DepositionJul 7, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Feb 13, 2013Group: Database references
Revision 1.3Apr 3, 2013Group: Database references

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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: Histone H4


Theoretical massNumber of molelcules
Total (without water)15,6692
Polymers15,6692
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 / 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: UNP 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 Histone H4


Mass: 1724.044 Da / Num. of mol.: 1 / Fragment: UNP residues 15-28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62805

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1513D HNCA
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HNCO
1913D HN(CA)CO
11013D C(CO)NH
11113D (H)CCH-TOCSY
11213D HBHA(CO)NH
11313D 1H-15N TOCSY
11413D 1H-15N NOESY
11513D 1H-13C NOESY aliphatic
11613D 1H-13C NOESY aromatic
11723D 13C/15N-filtered, 13C-edited NOESY
11832D 1H-15N HSQC
11932D 1H-13C HSQC
12033D (H)CCH-TOCSY
12143D 13C/15N-filtered, 13C-edited NOESY
12233D 1H-15N NOESY
12333D 1H-13C NOESY
12412D (HB)CB(CGCD)HD

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Sample preparation

Details
Solution-IDContentsSolvent system
11.7 mM [U-100% 13C; U-100% 15N] protein_1, 8.5 mM protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 90% H2O/10% D2O90% H2O/10% D2O
21.7 mM [U-100% 13C; U-100% 15N] protein_1, 8.5 mM protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 100% D2O100% D2O
35 mM protein_1, 4 mM [U-100% 13C; U-100% 15N] protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 90% H2O/10% D2O90% H2O/10% D2O
45 mM protein_1, 4 mM [U-100% 13C; U-100% 15N] protein_2, 25 mM sodium phosphate, 0.001 % DSS, 0.001 % NaN3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.7 mMentity_1-1[U-100% 13C; U-100% 15N]1
8.5 mMentity_2-21
25 mMsodium phosphate-31
0.001 %DSS-41
0.001 %NaN3-51
1.7 mMentity_1-6[U-100% 13C; U-100% 15N]2
8.5 mMentity_2-72
25 mMsodium phosphate-82
0.001 %DSS-92
0.001 %NaN3-102
5 mMentity_1-113
4 mMentity_2-12[U-100% 13C; U-100% 15N]3
25 mMsodium phosphate-133
0.001 %DSS-143
0.001 %NaN3-153
5 mMentity_1-164
4 mMentity_2-17[U-100% 13C; U-100% 15N]4
25 mMsodium phosphate-184
0.001 %DSS-194
0.001 %NaN3-204
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
xwinnmrBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
SANEDuggan, Legge, Dyson & Wrightchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
CSIWishart, D.S.data analysis
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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