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- PDB-3lgf: Crystal structure of the 53BP1 tandem tudor domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3lgf
TitleCrystal structure of the 53BP1 tandem tudor domain in complex with p53K370me2
Components
  • DIMETHYLATED p53 Lysine 370 PEPTIDE
  • Tumor suppressor p53-binding protein 1
KeywordsCELL CYCLE / tandem tudor domains / dimethylated p53 peptide / dna repair / DNA damage / DNA-binding / Methylation / Transcription / Transcription regulation
Function / homology
Function and homology information


ubiquitin modification-dependent histone binding / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / DNA repair complex / negative regulation of double-strand break repair via homologous recombination / telomeric DNA binding / SUMOylation of transcription factors / methylated histone binding / histone reader activity ...ubiquitin modification-dependent histone binding / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / DNA repair complex / negative regulation of double-strand break repair via homologous recombination / telomeric DNA binding / SUMOylation of transcription factors / methylated histone binding / histone reader activity / replication fork / DNA damage checkpoint signaling / transcription coregulator activity / Nonhomologous End-Joining (NHEJ) / protein homooligomerization / G2/M DNA damage checkpoint / kinetochore / double-strand break repair via nonhomologous end joining / positive regulation of DNA-binding transcription factor activity / p53 binding / site of double-strand break / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / damaged DNA binding / 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
: / 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 / SH3 type barrels. / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRoy, S. / Kutateladze, T.G.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural insight into p53 recognition by the 53BP1 tandem Tudor domain.
Authors: Roy, S. / Musselman, C.A. / Kachirskaia, I. / Hayashi, R. / Glass, K.C. / Nix, J.C. / Gozani, O. / Appella, E. / Kutateladze, T.G.
History
DepositionJan 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Tumor suppressor p53-binding protein 1
B: DIMETHYLATED p53 Lysine 370 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5575
Polymers15,1602
Non-polymers3963
Water2,612145
1
A: Tumor suppressor p53-binding protein 1
B: DIMETHYLATED p53 Lysine 370 PEPTIDE
hetero molecules

A: Tumor suppressor p53-binding protein 1
B: DIMETHYLATED p53 Lysine 370 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,11310
Polymers30,3204
Non-polymers7936
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3560 Å2
ΔGint-18 kcal/mol
Surface area13360 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-6 kcal/mol
Surface area7650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.440, 78.100, 36.310
Angle α, β, γ (deg.)90.00, 121.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-9-

HOH

21A-41-

HOH

31A-108-

HOH

41A-110-

HOH

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Components

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


Mass: 14029.840 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: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12888
#2: Protein/peptide DIMETHYLATED p53 Lysine 370 PEPTIDE


Mass: 1130.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES-Na pH 7.0, 2% PEG 400 and 2.4 M ammonium sulphate., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jan 10, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→39.05 Å / Num. all: 75227 / Num. obs: 21342 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Redundancy: 3.52 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2136 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 2009_02_15_2320_3)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G3R
Resolution: 1.5→39.05 Å / SU ML: 0.51 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 1092 5.13 %RANDOM
Rwork0.2166 ---
all0.224 21342 --
obs0.2174 21283 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.114 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.3683 Å2-0 Å2-6.2167 Å2
2---6.0044 Å20 Å2
3---9.3727 Å2
Refine analyzeLuzzati sigma a obs: 0.208 Å
Refinement stepCycle: LAST / Resolution: 1.5→39.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 25 145 1133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131058
X-RAY DIFFRACTIONf_angle_d1.4111420
X-RAY DIFFRACTIONf_dihedral_angle_d17.64397
X-RAY DIFFRACTIONf_chiral_restr0.099143
X-RAY DIFFRACTIONf_plane_restr0.006181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.56830.31331360.30592525X-RAY DIFFRACTION100
1.5683-1.6510.31391410.25382504X-RAY DIFFRACTION100
1.651-1.75440.2681370.22862514X-RAY DIFFRACTION100
1.7544-1.88990.2311210.22192552X-RAY DIFFRACTION100
1.8899-2.080.28021530.23582471X-RAY DIFFRACTION99
2.08-2.3810.2531300.23492534X-RAY DIFFRACTION99
2.381-2.99960.22571340.20852557X-RAY DIFFRACTION100
2.9996-39.06320.1871400.18862534X-RAY DIFFRACTION99

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