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- PDB-6rmm: Crystal structure of TOPBP1 BRCT4,5 in complex with a 53BP1 phosp... -

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Basic information

Entry
Database: PDB / ID: 6rmm
TitleCrystal structure of TOPBP1 BRCT4,5 in complex with a 53BP1 phosphopeptide
Components
  • 53BP1TP53BP1
  • DNA topoisomerase 2-binding protein 1
KeywordsSIGNALING PROTEIN / BRCT domain Phosphopeptide recognition
Function / homology
Function and homology information


BRCA1-B complex / phosphorylation-dependent protein binding / ubiquitin-modified histone reader activity / chromatin-protein adaptor activity / positive regulation of isotype switching / cellular response to X-ray / homologous recombination / protein localization to site of double-strand break / DNA replication checkpoint signaling / double-strand break repair via alternative nonhomologous end joining ...BRCA1-B complex / phosphorylation-dependent protein binding / ubiquitin-modified histone reader activity / chromatin-protein adaptor activity / positive regulation of isotype switching / cellular response to X-ray / homologous recombination / protein localization to site of double-strand break / DNA replication checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / double-strand break repair via classical nonhomologous end joining / mitotic DNA replication checkpoint signaling / DNA repair complex / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA metabolic process / negative regulation of double-strand break repair via homologous recombination / response to ionizing radiation / telomeric DNA binding / site of DNA damage / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / SUMOylation of transcription factors / DNA replication initiation / chromosome organization / methylated histone binding / histone reader activity / protein serine/threonine kinase activator activity / replication fork / DNA damage checkpoint signaling / condensed nuclear chromosome / male germ cell nucleus / transcription coregulator activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / protein homooligomerization / G2/M DNA damage checkpoint / PML body / kinetochore / double-strand break repair via nonhomologous end joining / spindle pole / positive regulation of DNA-binding transcription factor activity / actin cytoskeleton / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / chromosome / Processing of DNA double-strand break ends / histone binding / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA repair / centrosome / DNA damage response / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / Secretoglobin superfamily / : / BRCA1 C Terminus (BRCT) domain / Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / twin BRCT domain / : ...: / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / Secretoglobin superfamily / : / BRCA1 C Terminus (BRCT) domain / Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / twin BRCT domain / : / : / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ribosomal protein L2, domain 2 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TP53-binding protein 1 / DNA topoisomerase 2-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53 Å
AuthorsDay, M. / Oliver, A.W. / Pearl, L.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC302/A14532 United Kingdom
CitationJournal: Elife / Year: 2019
Title: Phosphorylation-mediated interactions with TOPBP1 couple 53BP1 and 9-1-1 to control the G1 DNA damage checkpoint.
Authors: Bigot, N. / Day, M. / Baldock, R.A. / Watts, F.Z. / Oliver, A.W. / Pearl, L.H.
History
DepositionMay 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: DNA topoisomerase 2-binding protein 1
B: DNA topoisomerase 2-binding protein 1
C: DNA topoisomerase 2-binding protein 1
D: DNA topoisomerase 2-binding protein 1
P: 53BP1
R: 53BP1


Theoretical massNumber of molelcules
Total (without water)89,2916
Polymers89,2916
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Fluorescence polarisation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-29 kcal/mol
Surface area39880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.810, 134.810, 303.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
DNA topoisomerase 2-binding protein 1 / DNA topoisomerase II-beta-binding protein 1 / TopBP1 / DNA topoisomerase II-binding protein 1


Mass: 21507.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOPBP1, KIAA0259 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92547
#2: Protein/peptide 53BP1 / TP53BP1


Mass: 1630.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12888*PLUS

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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: 4.45 Å3/Da / Density % sol: 72.37 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 4000, 20% v/v glycerol 0.02 M of each carboxylic acid 0.1 M MOPS/HEPES-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.53→67.405 Å / Num. obs: 20816 / % possible obs: 100 % / Redundancy: 70.6 % / Net I/σ(I): 21.03
Reflection shellResolution: 3.53→3.656 Å / Num. unique obs: 2034 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UEN

3uen


Resolution: 3.53→67.405 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.99
RfactorNum. reflection% reflection
Rfree0.2338 1047 5.03 %
Rwork0.221 --
obs0.2216 20813 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.53→67.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6078 0 0 0 6078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0236196
X-RAY DIFFRACTIONf_angle_d2.4448404
X-RAY DIFFRACTIONf_dihedral_angle_d3.9663726
X-RAY DIFFRACTIONf_chiral_restr0.124986
X-RAY DIFFRACTIONf_plane_restr0.021062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5301-3.71620.33341420.33362760X-RAY DIFFRACTION100
3.7162-3.9490.29271350.31562762X-RAY DIFFRACTION100
3.949-4.25390.29811560.28042757X-RAY DIFFRACTION100
4.2539-4.68190.28641610.25852766X-RAY DIFFRACTION100
4.6819-5.35910.25591430.22382811X-RAY DIFFRACTION100
5.3591-6.75090.27151520.22782864X-RAY DIFFRACTION100
6.7509-67.41730.1581580.16273046X-RAY DIFFRACTION100

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