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- PDB-1xni: Tandem Tudor Domain of 53BP1 -

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Basic information

Entry
Database: PDB / ID: 1xni
TitleTandem Tudor Domain of 53BP1
ComponentsTumor suppressor p53-binding protein 1
KeywordsCELL CYCLE / beta-barrel / bent beta-sheet
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 double-strand break repair via homologous recombination / methylated histone binding ...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 double-strand break repair via homologous recombination / methylated histone binding / histone reader activity / DNA damage checkpoint signaling / replication fork / Nonhomologous End-Joining (NHEJ) / positive regulation of DNA-binding transcription factor activity / transcription coregulator activity / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / double-strand break repair via nonhomologous end joining / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA damage response / positive 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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.8 Å
AuthorsHuyen, Y. / Zgheib, O. / DiTullio Jr., R.A. / Gorgoulis, V.G. / Zacharatos, P. / Petty, T.J. / Sheston, E.A. / Mellert, H.S. / Stavridi, E.S. / Halazonetis, T.D.
CitationJournal: Nature / Year: 2004
Title: Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks
Authors: Huyen, Y. / Zgheib, O. / DiTullio Jr., R.A. / Gorgoulis, V.G. / Zacharatos, P. / Petty, T.J. / Sheston, E.A. / Mellert, H.S. / Stavridi, E.S. / Halazonetis, T.D.
History
DepositionOct 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor suppressor p53-binding protein 1
B: Tumor suppressor p53-binding protein 1
C: Tumor suppressor p53-binding protein 1
D: Tumor suppressor p53-binding protein 1
E: Tumor suppressor p53-binding protein 1
F: Tumor suppressor p53-binding protein 1
G: Tumor suppressor p53-binding protein 1
H: Tumor suppressor p53-binding protein 1
I: Tumor suppressor p53-binding protein 1
J: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)134,47210
Polymers134,47210
Non-polymers00
Water00
1
A: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,4471
Polymers13,4471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,4471
Polymers13,4471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,4471
Polymers13,4471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,4471
Polymers13,4471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,4471
Polymers13,4471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,4471
Polymers13,4471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,4471
Polymers13,4471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,4471
Polymers13,4471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,4471
Polymers13,4471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,4471
Polymers13,4471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.610, 157.664, 179.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 13447.231 Da / Num. of mol.: 10 / Fragment: residues 1485-1602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q12888

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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: 3.15 Å3/Da / Density % sol: 60.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 3350, magnesium nitrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 3, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 51072 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 46.1 Å2
Reflection shellResolution: 2.8→2.89 Å / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1142674.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 4950 10.1 %RANDOM
Rwork0.247 ---
all-50821 --
obs-48979 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.7136 Å2 / ksol: 0.353286 e/Å3
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.96 Å20 Å20 Å2
2--1.53 Å20 Å2
3----9.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9480 0 0 0 9480
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 735 9.9 %
Rwork0.331 6695 -
obs--89 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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