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- PDB-5z78: Structure of TIRR/53BP1 complex -

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Basic information

Entry
Database: PDB / ID: 5z78
TitleStructure of TIRR/53BP1 complex
Components
  • TP53-binding protein 1
  • Tudor-interacting repair regulator protein
KeywordsTRANSCRIPTION/PROTEIN BINDING / DNA repair protein / TRANSCRIPTION-PROTEIN BINDING complex
Function / homology
Function and homology information


negative regulation of double-strand break repair via nonhomologous end joining / 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 / snoRNA binding / telomeric DNA binding / SUMOylation of transcription factors ...negative regulation of double-strand break repair via nonhomologous end joining / 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 / snoRNA binding / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / methylated histone binding / histone reader activity / replication fork / DNA damage checkpoint signaling / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / positive regulation of DNA-binding transcription factor activity / 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 / 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 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase ...: / 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 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / breast cancer carboxy-terminal domain / NUDIX hydrolase-like domain superfamily / BRCT domain profile. / BRCT domain / BRCT domain superfamily / SH3 type barrels. / Ribosomal protein L2, domain 2 / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TP53-binding protein 1 / Tudor-interacting repair regulator protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.762 Å
AuthorsDai, Y.X. / Shan, S.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Ministry of Science and Technology2015CB856200 China
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for recognition of 53BP1 tandem Tudor domain by TIRR
Authors: Dai, Y. / Zhang, A. / Shan, S. / Gong, Z. / Zhou, Z.
History
DepositionJan 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 22, 2023Group: 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
B: Tudor-interacting repair regulator protein
A: Tudor-interacting repair regulator protein
C: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)60,4453
Polymers60,4453
Non-polymers00
Water2,126118
1
B: Tudor-interacting repair regulator protein
A: Tudor-interacting repair regulator protein


Theoretical massNumber of molelcules
Total (without water)46,5002
Polymers46,5002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-22 kcal/mol
Surface area18610 Å2
MethodPISA
2
C: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,9451
Polymers13,9451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.108, 167.108, 46.505
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Tudor-interacting repair regulator protein / NUDT16-like protein 1 / Protein syndesmos


Mass: 23250.016 Da / Num. of mol.: 2 / Fragment: UNP residues 6-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nudt16l1, Sdos, Tirr / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q8VHN8
#2: Protein TP53-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 K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q12888
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.21 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris propane,PEG MME550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.76→144.72 Å / Num. obs: 73765 / % possible obs: 99.9 % / Redundancy: 19.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 74.8
Reflection shellResolution: 1.76→1.82 Å / Num. unique obs: 7330 / Rpim(I) all: 0.645

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G3R,4ZG0

2g3r

4zg0


Resolution: 1.762→40.635 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 1982 2.69 %RANDOM
Rwork0.2057 ---
obs0.2062 73765 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.762→40.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 0 118 4192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084162
X-RAY DIFFRACTIONf_angle_d1.1675605
X-RAY DIFFRACTIONf_dihedral_angle_d14.4341544
X-RAY DIFFRACTIONf_chiral_restr0.052605
X-RAY DIFFRACTIONf_plane_restr0.005719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7616-1.80570.29891380.28785063X-RAY DIFFRACTION99
1.8057-1.85450.27291390.25415126X-RAY DIFFRACTION100
1.8545-1.9090.24961420.24765071X-RAY DIFFRACTION100
1.909-1.97070.23631430.23165083X-RAY DIFFRACTION100
1.9707-2.04110.24971390.21975112X-RAY DIFFRACTION100
2.0411-2.12280.22781420.22085104X-RAY DIFFRACTION100
2.1228-2.21940.20571420.21065118X-RAY DIFFRACTION100
2.2194-2.33640.24631390.21065101X-RAY DIFFRACTION100
2.3364-2.48280.20121430.21695105X-RAY DIFFRACTION100
2.4828-2.67440.24971390.21185112X-RAY DIFFRACTION100
2.6744-2.94350.23071400.2265186X-RAY DIFFRACTION100
2.9435-3.36930.20861470.21265140X-RAY DIFFRACTION100
3.3693-4.24420.21251440.19195200X-RAY DIFFRACTION100
4.2442-40.64570.21491450.18055262X-RAY DIFFRACTION99

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