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- PDB-8u4u: Crystal structure of 53BP1 tandem Tudor domain homodimer engineer... -

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Basic information

Entry
Database: PDB / ID: 8u4u
TitleCrystal structure of 53BP1 tandem Tudor domain homodimer engineered with two disulfide bridges
ComponentsTP53-binding protein 1
KeywordsSIGNALING PROTEIN / 53BP1 / DNA damage response / DNA double-strand break repair / non-homologous end joining / homologous recombination / chromatin-binding protein / engineered protein
Function / homology
Function and homology information


histone H4K20me2 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 / 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 ...histone H4K20me2 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 / 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 / : / positive regulation of DNA-binding transcription factor activity / DNA damage checkpoint signaling / replication fork / histone reader activity / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / G2/M DNA damage checkpoint / protein homooligomerization / kinetochore / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / histone 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
Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 Å
AuthorsCui, G. / Botuyan, M.V. / Thompson, J.R. / Mer, G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA132878 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136262 United States
Department of Defense (DOD, United States)W81XWH-20-1-0322/OC190394 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
DepositionSep 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation / citation_author
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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: TP53-binding protein 1
D: TP53-binding protein 1
E: TP53-binding protein 1
F: TP53-binding protein 1
G: TP53-binding protein 1
H: TP53-binding protein 1
I: TP53-binding protein 1
J: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)140,47010
Polymers140,47010
Non-polymers00
Water00
1
A: TP53-binding protein 1
B: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)28,0942
Polymers28,0942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-19 kcal/mol
Surface area12290 Å2
MethodPISA
2
C: TP53-binding protein 1
D: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)28,0942
Polymers28,0942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-19 kcal/mol
Surface area11960 Å2
MethodPISA
3
E: TP53-binding protein 1
F: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)28,0942
Polymers28,0942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-19 kcal/mol
Surface area12100 Å2
MethodPISA
4
G: TP53-binding protein 1
H: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)28,0942
Polymers28,0942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-20 kcal/mol
Surface area12150 Å2
MethodPISA
5
I: TP53-binding protein 1
J: TP53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)28,0942
Polymers28,0942
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-19 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.500, 161.825, 179.947
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
TP53-binding protein 1 / 53BP1 / p53-binding protein 1 / p53BP1


Mass: 14047.006 Da / Num. of mol.: 10 / Mutation: E1549C, E1567C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Plasmid: pHISPP / Production host: Escherichia coli (E. coli) / References: UniProt: Q12888
Has protein modificationY

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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: 3.76 Å3/Da / Density % sol: 67.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the ...Details: Crystals of the protein (15 mg/mL) were obtained by the hanging drop vapor diffusion method, mixing 1 microliter of the sample in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl and 1 microliter of the reservoir solution (0.1 M Bis-Tris, pH 6.5) at 293 K. The crystals were cryoprotected with 25% (w/v) xylitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.79→50 Å / Num. obs: 19541 / % possible obs: 89.41 % / Redundancy: 5.7 % / Biso Wilson estimate: 109.86 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1197 / Rpim(I) all: 0.05194 / Rrim(I) all: 0.1311 / Net I/σ(I): 15.7
Reflection shellResolution: 3.79→3.926 Å / Rmerge(I) obs: 0.6143 / Mean I/σ(I) obs: 3.23 / Num. unique obs: 1631 / CC1/2: 0.813 / Rpim(I) all: 0.2842 / Rrim(I) all: 0.6804

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.79→48.19 Å / SU ML: 0.5358 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3893
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2997 1943 9.99 %
Rwork0.2459 17514 -
obs0.2513 19457 89.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 142.67 Å2
Refinement stepCycle: LAST / Resolution: 3.79→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9490 0 0 0 9490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00169680
X-RAY DIFFRACTIONf_angle_d0.40413007
X-RAY DIFFRACTIONf_chiral_restr0.04361357
X-RAY DIFFRACTIONf_plane_restr0.0031650
X-RAY DIFFRACTIONf_dihedral_angle_d13.56063587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.79-3.880.39111100.3519996X-RAY DIFFRACTION73.05
3.88-3.990.31641190.30781079X-RAY DIFFRACTION77.94
3.99-4.10.34931190.27981080X-RAY DIFFRACTION78.99
4.1-4.240.34411230.26331100X-RAY DIFFRACTION79.52
4.24-4.390.26491240.22281117X-RAY DIFFRACTION81.32
4.39-4.560.28561320.21841190X-RAY DIFFRACTION85.57
4.56-4.770.31121350.24171218X-RAY DIFFRACTION88.14
4.77-5.020.29311430.22421282X-RAY DIFFRACTION92.35
5.02-5.330.31491490.24651341X-RAY DIFFRACTION96.13
5.33-5.750.29711530.2451390X-RAY DIFFRACTION98.85
5.75-6.320.3551540.26441387X-RAY DIFFRACTION99.16
6.32-7.230.29721590.26471435X-RAY DIFFRACTION99.56
7.24-9.110.29331570.23191420X-RAY DIFFRACTION99.31
9.11-48.190.2551660.22561479X-RAY DIFFRACTION97.51
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)
15.231277518851.688845766582.664028691264.69123934694-0.8337831929142.16870913155-0.097609104080.205345265388-0.33735452487-0.455030087575-0.0200410000002-0.5259082431390.3027800779440.5809155228360.1005075013271.211598042010.2340916900930.1016064174691.13422067315-0.09028545480781.1485228933811.3999157353-17.041978681-9.75319143218
25.92834952011-0.3856604171612.384769619756.87719883964-3.289152796616.23661128603-0.0617190362928-0.08556309101470.2635167690040.356914920097-0.01349797200880.829878937347-0.03931459190030.04536837071510.06028065671940.9293779596770.0255886671588-0.003608767710061.12706159498-0.1690280607691.01609454258-0.459210754501-22.4715024568-27.7360529994
37.946042096474.025957393660.4823308521995.200759891850.8984841135835.226605986570.18601945345-0.263449357633-0.274067785773-0.00258788911786-0.00711934824885-0.312493152347-0.0744532939187-0.518586171964-0.1454928653681.123235778750.03669829698310.0563790808430.961217053008-0.008707165420471.0460932658920.3074990071-57.3557602286-22.3580785697
48.867697140910.85236219354-2.72721416913.951690956581.00546141787.84407126430.0544335220128-0.05799978100310.5067570096590.6943703953720.0762948590556-0.4513410810010.1514356137880.382299713851-0.1129668920440.994010307261-0.0292617153256-0.1093132780310.94521122260.09674149202071.0060972243132.6076292677-42.6406963152-32.5493373302
55.570254557560.00578735310346-0.9211473009742.90060394651-2.703002183356.915202614060.17085018369-0.61362496609-0.4676091381950.338489209023-0.174174819704-0.6672876633720.3305296039270.2069765735040.004767044239541.08575728605-0.18706218903-0.09175859093061.30092003522-0.1057766643541.4857746656326.3368558424.03234849482.60112671114
66.36928242362.549007666260.5831478764696.442870270891.867556173196.89121322347-0.398180489068-0.4609905216640.04366721579810.6568203665730.2370956387420.00985628549845-0.149494886310.4430623961970.1066725787621.198320623440.04865095448070.08965405899861.12698241576-0.01112700635621.1171784107315.25077782865.064062238745.06105344878
77.44711710458-2.26096028316-1.781279202776.20922759278-0.1205449784836.09211642197-0.411337054076-0.02816970787390.117181824160.218976264389-0.00485531839986-0.7872631795090.03574422032240.5885505922340.3346011465470.982417495109-0.04265795322550.02939795776161.043592971020.04026459032851.1366604807944.5025702022-37.1183642123-75.4983853026
85.563557176343.27310208307-2.46558170827.92738828771-3.376418034243.31790000673-0.224615023250.3687290000360.0150066114531-0.2168447118870.0222628092407-0.2714732561740.106823859739-0.1416655896270.1508866656241.008305471510.190064426723-0.01189954983421.168500511470.01606839075450.97747733718434.3555380913-32.6442903651-56.5121687817
95.22478568274-0.3775089524610.3719485416493.94514923219-0.4602912088955.76358244908-0.04598491368940.1021344710040.151977724742-1.11393571079-0.292098766172-0.004758244736510.1186707513880.1766912553160.2382758705661.539794865990.242813473392-0.1526655172481.257102165840.05815355547121.255933395-3.0034196201-15.7563389522-52.5517110873
105.11102499526-0.960967758012-0.5544189326754.333213332370.5025205917983.52336240055-0.3097085786010.2793368048210.0151057691251-0.4227726420760.1007409510440.4757449293880.54791700168-0.03481726922420.143945119131.551761808130.147055000405-0.3299499367491.283449725880.02516699391491.47355492495-14.8470137375-2.19463235409-65.2653217829
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1484 through 1602)AA1484 - 16021 - 119
22(chain 'B' and resid 1484 through 1602)BB1484 - 16021 - 119
33(chain 'C' and resid 1484 through 1602)CC1484 - 16021 - 119
44(chain 'D' and resid 1484 through 1602)DD1484 - 16021 - 119
55(chain 'E' and resid 1484 through 1602)EE1484 - 16021 - 119
66(chain 'F' and resid 1484 through 1603)FF1484 - 16031 - 120
77(chain 'G' and resid 1484 through 1603)GG1484 - 16031 - 120
88(chain 'H' and resid 1484 through 1603)HH1484 - 16031 - 120
99(chain 'I' and resid 1484 through 1602)II1484 - 16021 - 119
1010(chain 'J' and resid 1484 through 1602)JJ1484 - 16021 - 119

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