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- PDB-6my0: Structure of 53BP1 Tandem Tudor domains with E1549P and D1550N mu... -

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Basic information

Entry
Database: PDB / ID: 6my0
TitleStructure of 53BP1 Tandem Tudor domains with E1549P and D1550N mutations
ComponentsTP53-binding protein 1
KeywordsPROTEIN BINDING / 53BP1 / DNA damage response / DNA double-strand breaks / Tudor domain
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 / 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-modified histone reader activity / 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 / 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
: / 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
TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCui, G. / Botuyan, M.V. / Mer, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA132878 United States
Other privateW81XWH-16-1-0391 United States
CitationJournal: Nat Commun / Year: 2023
Title: An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering.
Authors: Cui, G. / Botuyan, M.V. / Drane, P. / Hu, Q. / Bragantini, B. / Thompson, J.R. / Schuller, D.J. / Detappe, A. / Perfetti, M.T. / James, L.I. / Frye, S.V. / Chowdhury, D. / Mer, G.
History
DepositionOct 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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: TP53-binding protein 1
B: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)27,8242
Polymers27,8242
Non-polymers00
Water2,324129
1
A: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,9121
Polymers13,9121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,9121
Polymers13,9121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.100, 141.270, 47.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein TP53-binding protein 1 / p53BP1


Mass: 13911.797 Da / Num. of mol.: 2 / Mutation: E1549P, D1550N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Plasmid: pTEV / Production host: Escherichia coli (E. coli) / References: UniProt: Q12888
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.5 M sodium/potassium phosphate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.2→39.587 Å / Num. obs: 12755 / % possible obs: 98.58 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.08728 / Rpim(I) all: 0.02645 / Rrim(I) all: 0.09134 / Net I/σ(I): 23.43
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.5531 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 1078 / Rpim(I) all: 0.171 / Rrim(I) all: 0.5797 / % possible all: 87.36

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G3R

2g3r


Resolution: 2.2→39.587 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.77
RfactorNum. reflection% reflection
Rfree0.233 1260 10 %
Rwork0.1873 --
obs0.192 12596 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→39.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 0 129 1985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021929
X-RAY DIFFRACTIONf_angle_d0.542609
X-RAY DIFFRACTIONf_dihedral_angle_d10.0111137
X-RAY DIFFRACTIONf_chiral_restr0.047278
X-RAY DIFFRACTIONf_plane_restr0.003335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.28810.30251230.20911108X-RAY DIFFRACTION88
2.2881-2.39220.28051380.20921239X-RAY DIFFRACTION100
2.3922-2.51830.2461400.19481263X-RAY DIFFRACTION100
2.5183-2.67610.2711390.20911245X-RAY DIFFRACTION100
2.6761-2.88260.2311400.18911263X-RAY DIFFRACTION100
2.8826-3.17260.21161420.17031281X-RAY DIFFRACTION100
3.1726-3.63140.21851430.16911286X-RAY DIFFRACTION100
3.6314-4.57410.1881440.1531292X-RAY DIFFRACTION100
4.5741-39.59350.25051510.22061359X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.83720.53470.18455.5349-2.81935.78160.0509-0.0270.08450.2152-0.1395-0.2016-0.43450.11490.09410.15720.0462-0.00980.1456-0.02970.120920.287635.549151.2845
24.4238-1.81592.55482.4934-0.07632.80780.2076-0.0568-0.34070.5628-0.02180.2250.5383-0.3131-0.13290.3219-0.04070.04630.1628-0.02560.163813.094219.561847.7677
36.60391.36020.89653.49320.95623.50530.1979-0.0488-0.30880.3681-0.1167-0.2130.4774-0.0042-0.03680.27160.02510.0050.1478-0.02330.099715.638420.417748.3321
42.77681.4317-0.46264.2338-1.41723.24820.104-0.1133-0.3110.063-0.2518-0.4382-0.13560.67960.07710.1365-0.001-0.01690.2014-0.01270.203125.874116.417370.1459
53.4569-1.314-1.1756.1980.94512.0459-0.0097-0.1585-0.20270.3758-0.11090.27890.345-0.14930.08540.165-0.0673-0.00860.12170.0030.118610.060411.322377.555
65.30170.6050.25245.09161.73575.4752-0.0520.0374-0.09010.1682-0.0140.3170.2362-0.41020.03920.1311-0.008-0.02140.0812-0.0110.12559.4148.803375.4017
76.0887-1.3002-0.75643.5843-0.22470.13790.0121-1.0061-0.26260.49480.1373-0.68190.40660.69950.10740.28680.1253-0.13140.47430.060.377427.021710.48580.4358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1482 through 1531 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1532 through 1564 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1565 through 1603 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1485 through 1542 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1543 through 1564 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1565 through 1589 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1590 through 1602 )

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