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- PDB-2ig0: Structure of 53BP1/methylated histone peptide complex -

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Basic information

Entry
Database: PDB / ID: 2ig0
TitleStructure of 53BP1/methylated histone peptide complex
Components
  • Dimethylated Histone H4-K20 peptide
  • Tumor suppressor p53-binding protein 1
KeywordsCELL CYCLE / TANDEM TUDOR DOMAINS / DIMETHYLATED HISTONE H4 / DNA REPAIR / CELL CYCLE REGULATION
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 / protein localization to CENP-A containing chromatin ...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 / protein localization to CENP-A containing chromatin / negative regulation of double-strand break repair via homologous recombination / 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 / methylated histone binding / Meiotic synapsis / histone reader activity / 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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / replication fork / DNA damage checkpoint signaling / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / Transcriptional regulation by small RNAs / 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 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / protein homooligomerization / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / kinetochore / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / positive regulation of DNA-binding transcription factor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / double-strand break repair via nonhomologous end joining / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / p53 binding / 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 / chromosome, telomeric region / damaged DNA binding / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMer, G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Structural Basis for the Methylation State-Specific Recognition of Histone H4-K20 by 53BP1 and Crb2 in DNA Repair.
Authors: Botuyan, M.V. / Lee, J. / Ward, I.M. / Kim, J.E. / Thompson, J.R. / Chen, J. / Mer, G.
History
DepositionSep 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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: Dimethylated Histone H4-K20 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3953
Polymers15,2992
Non-polymers961
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.372, 78.535, 36.445
Angle α, β, γ (deg.)90.00, 121.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-65-

HOH

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Components

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


Mass: 13944.780 Da / Num. of mol.: 1 / Fragment: tandem tudor domains (resiudes 1484-1603)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Plasmid: PTEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12888
#2: Protein/peptide Dimethylated Histone H4-K20 peptide


Mass: 1354.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P62805*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2% PEG 400, 0.1M HEPES/NA, 2M AMMONIUM SULFATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→24.11 Å / Num. all: 11776 / Num. obs: 11776 / % possible obs: 82.96 %
Reflection shellResolution: 1.7→1.744 Å / % possible all: 30.34

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.11 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.55 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25138 629 5.1 %RANDOM
Rwork0.1759 ---
obs0.1798 11775 82.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.516 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.03 Å2
2---0.18 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 5 191 1315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221159
X-RAY DIFFRACTIONr_angle_refined_deg2.2231.9871581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1265153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03423.39356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09815210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5631510
X-RAY DIFFRACTIONr_chiral_restr0.1890.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02923
X-RAY DIFFRACTIONr_nbd_refined0.3010.2575
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2790
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3150.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4110.227
X-RAY DIFFRACTIONr_mcbond_it1.6011.5716
X-RAY DIFFRACTIONr_mcangle_it2.44721130
X-RAY DIFFRACTIONr_scbond_it3.7143511
X-RAY DIFFRACTIONr_scangle_it5.1034.5450
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 15 -
Rwork0.197 320 -
obs--30.34 %

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