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- PDB-5zcj: Crystal structure of complex -

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Basic information

Entry
Database: PDB / ID: 5zcj
TitleCrystal structure of complex
Components
  • TP53-binding protein 1
  • Tudor-interacting repair regulator protein
KeywordsPROTEIN 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 / RNA binding / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsWang, J. / Yuan, Z. / Cui, Y. / Xie, R. / Wang, M. / Ma, Y. / Yu, X. / Liu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81672794 China
CitationJournal: To Be Published
Title: Crystal structure of complex
Authors: Wang, J. / Yuan, Z. / Cui, Y. / Xie, R. / Wang, M. / Ma, Y. / Yu, X. / Liu, X.
History
DepositionFeb 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: Tudor-interacting repair regulator protein
B: Tudor-interacting repair regulator protein
C: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)66,1583
Polymers66,1583
Non-polymers00
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-26 kcal/mol
Surface area23910 Å2
Unit cell
Length a, b, c (Å)111.144, 103.922, 61.470
Angle α, β, γ (deg.)90.00, 95.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23206.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16L1, SDOS, TIRR / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BRJ7
#2: Protein TP53-binding protein 1 / p53BP1


Mass: 19746.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12888
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.7 M Ammonium tartrate, 0.1 M Sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→19.92 Å / Num. obs: 308418 / % possible obs: 97.35 % / Redundancy: 6.7 % / Net I/σ(I): 13.94
Reflection shellResolution: 2→2.07 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2932)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.004→19.917 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 21.81
RfactorNum. reflection% reflection
Rfree0.2189 1966 4.33 %
Rwork0.1899 --
obs0.1912 45400 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.004→19.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 0 393 4509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024221
X-RAY DIFFRACTIONf_angle_d0.5095698
X-RAY DIFFRACTIONf_dihedral_angle_d4.9333278
X-RAY DIFFRACTIONf_chiral_restr0.038624
X-RAY DIFFRACTIONf_plane_restr0.003732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.004-2.05410.28891330.25493017X-RAY DIFFRACTION95
2.0541-2.10960.28441330.2422953X-RAY DIFFRACTION94
2.1096-2.17160.23551390.2273004X-RAY DIFFRACTION95
2.1716-2.24160.25371410.20743110X-RAY DIFFRACTION98
2.2416-2.32160.2521380.2023105X-RAY DIFFRACTION98
2.3216-2.41440.22931430.20443130X-RAY DIFFRACTION99
2.4144-2.52410.2311410.2013142X-RAY DIFFRACTION99
2.5241-2.65680.24661430.19383132X-RAY DIFFRACTION99
2.6568-2.82290.2261420.19033141X-RAY DIFFRACTION98
2.8229-3.04010.19611420.18153098X-RAY DIFFRACTION97
3.0401-3.34480.21331410.17253105X-RAY DIFFRACTION98
3.3448-3.82580.20671440.16473178X-RAY DIFFRACTION99
3.8258-4.80880.18541430.1533158X-RAY DIFFRACTION99
4.8088-19.91780.19141430.20293161X-RAY DIFFRACTION98

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