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- PDB-6mxy: Structure of 53BP1 tandem Tudor domains in complex with small mol... -

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Basic information

Entry
Database: PDB / ID: 6mxy
TitleStructure of 53BP1 tandem Tudor domains in complex with small molecule UNC3351
ComponentsTP53-binding protein 1
KeywordsPROTEIN BINDING / DNA damage response / Tudor domain / 53BP1 / small molecule inhibitor
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 / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / methylated histone binding ...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 / 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 / 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
Chem-K6M / PHOSPHATE ION / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.624 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6678
Polymers27,8902
Non-polymers7776
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-40 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.570, 60.570, 138.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein TP53-binding protein 1 / p53BP1


Mass: 13944.780 Da / Num. of mol.: 2
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: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K6M / N-[3-(tert-butylamino)propyl]-3-(trifluoromethyl)benzamide


Mass: 302.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21F3N2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic, pH 5.6; 1M ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6299 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6299 Å / Relative weight: 1
ReflectionResolution: 1.624→18.48 Å / Num. obs: 37788 / % possible obs: 99.67 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.07398 / Rpim(I) all: 0.02217 / Rrim(I) all: 0.07734 / Net I/σ(I): 30.61
Reflection shellResolution: 1.624→1.682 Å / Redundancy: 8 % / Rmerge(I) obs: 0.7412 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3659 / Rpim(I) all: 0.2749 / Rrim(I) all: 0.7922 / % possible all: 97.97

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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: 1.624→18.48 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.63
RfactorNum. reflection% reflection
Rfree0.2128 1985 5.25 %
Rwork0.179 --
obs0.1807 37781 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.624→18.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 46 348 2349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192083
X-RAY DIFFRACTIONf_angle_d1.4632815
X-RAY DIFFRACTIONf_dihedral_angle_d10.4741233
X-RAY DIFFRACTIONf_chiral_restr0.083287
X-RAY DIFFRACTIONf_plane_restr0.011358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6244-1.6650.28081370.24932463X-RAY DIFFRACTION97
1.665-1.70990.29191400.22422484X-RAY DIFFRACTION100
1.7099-1.76020.22181350.21242546X-RAY DIFFRACTION100
1.7602-1.8170.24911390.20812514X-RAY DIFFRACTION100
1.817-1.88190.25121460.20812545X-RAY DIFFRACTION100
1.8819-1.95710.25041420.19852541X-RAY DIFFRACTION100
1.9571-2.04610.21451360.18522516X-RAY DIFFRACTION100
2.0461-2.15380.2091440.17782544X-RAY DIFFRACTION100
2.1538-2.28850.19951390.17062562X-RAY DIFFRACTION100
2.2885-2.46490.2191440.17112557X-RAY DIFFRACTION100
2.4649-2.71220.21271420.16782565X-RAY DIFFRACTION100
2.7122-3.10310.19781460.16892591X-RAY DIFFRACTION100
3.1031-3.90350.17661470.15482621X-RAY DIFFRACTION100
3.9035-18.4810.19551480.16512747X-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)
15.39961.65471.62045.6172-1.46911.24270.1030.44550.732-0.4256-0.0433-0.2243-0.66420.4207-0.06560.2599-0.10830.11070.1589-0.00380.13931.241841.0692-20.16
21.55811.7653-0.86664.8674-1.84962.35570.0632-0.2218-0.27470.2408-0.2825-0.46340.24330.10230.23880.1579-0.08590.01380.0906-0.00090.0763-5.721623.2553-10.1067
30.64370.3773-0.34750.77270.05440.30950.0453-0.06530.00550.00250.0049-0.079-0.04390.0865-0.04650.1155-0.12210.02770.0442-0.0710.0289-0.171131.6408-11.1556
40.20850.0497-0.06680.17740.03850.19940.0463-0.0242-0.06510.0221-0.0170.04150.01220.02560.01030.1209-0.13540.02680.0265-0.02330.0563-10.615424.1788-12.7118
52.8996-2.32860.09664.20210.5643.66160.06030.10210.3259-0.3997-0.0618-0.2589-0.31370.12390.00390.1008-0.0754-0.03480.07620.01080.0775-20.394725.9783-22.1945
62.2242-0.01890.36061.0330.01981.28430.0135-0.00490.06040.0126-0.02820.1848-0.0604-0.07890.0540.0832-0.1219-0.0182-0.001-0.02210.0542-21.382625.867-16.6395
73.43871.05680.02072.95310.13833.20590.00480.1737-0.441-0.1509-0.0106-0.03910.3912-0.06380.0080.139-0.0210.03160.0548-0.06340.097-4.213819.269-21.0389
82.0234-0.4295-0.28271.899-0.44231.30980.0561-0.1588-0.13050.1463-0.1185-0.0618-0.06670.1340.06350.1542-0.26760.11970.04070.06760.0093-15.087922.68178.8195
90.14950.3277-1.06923.8357-2.35097.63760.1182-0.3412-0.13040.5225-0.508-0.52720.03520.59510.40220.1827-0.1406-0.02460.21650.06680.0987-10.98418.33049.6569
100.878-0.1574-0.490.610.0851.95970.1157-0.2464-0.02170.2206-0.122-0.0839-0.02540.1891-0.01070.1364-0.15260.0190.13540.02110.0684-10.147722.13265.7977
111.44371.3697-0.80211.5958-1.46452.11630.1086-0.04370.19070.26060.11390.2792-0.3581-0.0907-0.24190.293-0.1350.15370.153-0.02260.1468-23.541330.9459.8029
123.53870.5879-3.83951.4353-0.13235.53040.2099-0.20160.23270.09610.00160.0396-0.39180.2777-0.21030.2271-0.09870.08830.0762-0.03610.1338-15.714839.3691-3.9498
136.82316.82841.76178.60561.37311.1864-0.15260.1857-0.1487-0.14390.10870.29010.059-0.22290.07070.317-0.06650.22660.1865-0.06270.4441-29.687534.62970.9795
143.36760.57780.65367.0882-0.49263.6487-0.23370.14930.1649-0.26010.26520.4212-0.20770.05620.0010.179-0.05020.10560.0944-0.00120.2807-27.915933.413-1.9012
152.4594-0.05270.91061.9855-0.37412.2057-0.1210.09940.4282-0.07410.12960.3363-0.4322-0.0285-0.03850.2421-0.080.10020.03110.01230.2203-23.925636.8735-1.8076
163.16081.9346-1.0894.4761-2.6481.56760.1548-0.47890.02310.7736-0.10210.2564-0.24940.0055-0.0620.5212-0.17770.0880.2565-0.02910.1734-15.788334.240514.6237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1481 through 1489 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1490 through 1500 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1501 through 1519 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1520 through 1554 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1555 through 1563 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1564 through 1589 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1590 through 1603 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1482 through 1509 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1510 through 1519 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1520 through 1531 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1532 through 1542 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1543 through 1554 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1555 through 1564 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1565 through 1574 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1575 through 1589 )
16X-RAY DIFFRACTION16chain 'B' and (resid 1590 through 1603 )

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