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- PDB-8t2d: Ubiquitin variant i53:Mutant T12Y.T14E.L67R with 53BP1 Tudor domain -

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Basic information

Entry
Database: PDB / ID: 8t2d
TitleUbiquitin variant i53:Mutant T12Y.T14E.L67R with 53BP1 Tudor domain
Components
  • Tumor protein p53 binding protein 1
  • Ubiquitin variant i53
KeywordsPROTEIN BINDING / inhibitor
Function / homology
Function and homology information


nuclear body / DNA damage response / nucleoplasm / 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 ...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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ribosomal protein L2, domain 2 / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Tumor protein p53 binding protein 1 / Ubiquitin B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsPartridge, J.R. / Holden, J.K. / Wibowo, A.S. / Mulichak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2024
Title: Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair.
Authors: Perez-Bermejo, J.A. / Efagene, O. / Matern, W.M. / Holden, J.K. / Kabir, S. / Chew, G.M. / Andreoletti, G. / Catton, E. / Ennis, C.L. / Garcia, A. / Gerstenberg, T.L. / Hill, K.A. / Jain, A. ...Authors: Perez-Bermejo, J.A. / Efagene, O. / Matern, W.M. / Holden, J.K. / Kabir, S. / Chew, G.M. / Andreoletti, G. / Catton, E. / Ennis, C.L. / Garcia, A. / Gerstenberg, T.L. / Hill, K.A. / Jain, A. / Krassovsky, K. / Lalisan, C.D. / Lord, D. / Quejarro, B.J. / Sales-Lee, J. / Shah, M. / Silva, B.J. / Skowronski, J. / Strukov, Y.G. / Thomas, J. / Veraz, M. / Vijay, T. / Wallace, K.A. / Yuan, Y. / Grogan, J.L. / Wienert, B. / Lahiri, P. / Treusch, S. / Dever, D.P. / Soros, V.B. / Partridge, J.R. / Seim, K.L.
History
DepositionJun 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ubiquitin variant i53
A: Tumor protein p53 binding protein 1


Theoretical massNumber of molelcules
Total (without water)22,7112
Polymers22,7112
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-8 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.511, 46.855, 91.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin variant i53


Mass: 8794.099 Da / Num. of mol.: 1 / Mutation: T12Y, T14E, L67R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: J3QS39
#2: Protein Tumor protein p53 binding protein 1


Mass: 13916.683 Da / Num. of mol.: 1 / Fragment: Tudor Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Production host: Escherichia coli (E. coli) / References: UniProt: A6NNK5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.93 Å3/Da / Density % sol: 36.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES pH 6.0, 0.2 M Trimethylamine N-oxide dehydrate, 13% w/v PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97939 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.751→29.85 Å / Num. obs: 17557 / % possible obs: 98.89 % / Redundancy: 6.6 % / Biso Wilson estimate: 33.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06022 / Rpim(I) all: 0.02474 / Rrim(I) all: 0.0653 / Net I/σ(I): 12.41
Reflection shellResolution: 1.751→1.813 Å / Redundancy: 3.8 % / Num. unique obs: 1636 / CC1/2: 0.386 / Rpim(I) all: 0.9374 / % possible all: 94.24

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Cootmodel building
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.751→29.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.124 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.15
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2725 843 4.818 %
Rwork0.2224 16654 -
all0.225 --
obs-17497 98.915 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.643 Å2
Baniso -1Baniso -2Baniso -3
1-0.232 Å20 Å2-0 Å2
2---0.488 Å20 Å2
3---0.255 Å2
Refinement stepCycle: LAST / Resolution: 1.751→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 0 0 38 1573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121561
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161521
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.6492096
X-RAY DIFFRACTIONr_angle_other_deg0.4521.5783513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.676512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26610299
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.7091073
X-RAY DIFFRACTIONr_chiral_restr0.0640.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02351
X-RAY DIFFRACTIONr_nbd_refined0.2170.2251
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21424
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2729
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2905
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.276
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2190.214
X-RAY DIFFRACTIONr_nbd_other0.230.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.22
X-RAY DIFFRACTIONr_mcbond_it2.933.066757
X-RAY DIFFRACTIONr_mcbond_other2.9293.06756
X-RAY DIFFRACTIONr_mcangle_it4.255.476941
X-RAY DIFFRACTIONr_mcangle_other4.2565.48942
X-RAY DIFFRACTIONr_scbond_it3.8363.585804
X-RAY DIFFRACTIONr_scbond_other3.8373.584804
X-RAY DIFFRACTIONr_scangle_it6.0246.3681155
X-RAY DIFFRACTIONr_scangle_other6.0216.3711156
X-RAY DIFFRACTIONr_lrange_it7.84133.921694
X-RAY DIFFRACTIONr_lrange_other7.84433.941692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.751-1.7960.407550.36511690.36613070.8810.88993.64960.368
1.796-1.8450.327500.3411310.33912170.8810.90497.04190.344
1.845-1.8980.372560.31711400.3212110.8960.91598.76140.317
1.898-1.9560.391590.33511040.33811850.8640.90798.14350.331
1.956-2.020.254530.28710790.28511340.9540.93899.82360.273
2.02-2.0910.331620.2710520.27411210.910.94899.37560.256
2.091-2.1690.258400.22910260.2310670.9610.96699.90630.205
2.169-2.2570.282530.2469740.24810320.9510.95999.51550.226
2.257-2.3570.281580.2219550.22410160.950.97199.70470.2
2.357-2.4710.277510.2138940.2179480.9560.97499.68350.192
2.471-2.6040.226420.2118610.2129070.9720.9799.5590.191
2.604-2.7610.265310.218330.2128640.9460.9721000.189
2.761-2.950.313400.2157700.2198100.9470.9691000.198
2.95-3.1830.268450.2187170.2217620.9550.971000.204
3.183-3.4830.27330.2286770.237120.9650.96899.71910.217
3.483-3.8880.297390.2136160.2186550.9490.971000.205
3.888-4.4760.207280.1795460.1815740.9710.9791000.183
4.476-5.4520.381200.1834790.1895000.9290.9899.80.193
5.452-7.5850.187150.2293880.2274060.9750.96999.26110.227
7.585-29.850.192130.2172420.2162550.9580.9681000.244
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)
10.18980.0563-0.63294.5365-1.02762.3078-0.0322-0.04340.0479-0.6390.19540.01930.32450.0868-0.16310.268-0.0596-0.03140.029-0.00780.0201-10.3117-3.7673-5.4841
20.54940.04170.3931.4887-0.24720.7662-0.02580.05810.109-0.1971-0.0655-0.15670.0432-0.01380.09130.17620.01120.03590.02710.02830.0592-11.52716.0583-15.4487
Refinement TLS groupSelection: ALL

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