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- PDB-5j26: Crystal structure of a 53BP1 Tudor domain in complex with a ubiqu... -

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Basic information

Entry
Database: PDB / ID: 5j26
TitleCrystal structure of a 53BP1 Tudor domain in complex with a ubiquitin variant
Components
  • Tumor suppressor p53-binding protein 1
  • Ubiquitin Variant i53
KeywordsPROTEIN BINDING / tudor domain ubiquitin variant
Function / homology
Function and homology information


ubiquitin-modified histone reader activity / positive regulation of isotype switching / histone H4K20me2 reader activity / cellular response to X-ray / response to insecticide / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / : ...ubiquitin-modified histone reader activity / positive regulation of isotype switching / histone H4K20me2 reader activity / cellular response to X-ray / response to insecticide / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / : / histone reader activity / SUMOylation of transcription factors / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of double-strand break repair via homologous recombination / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / cytosolic ribosome / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / DNA damage checkpoint signaling / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / replication fork / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / transcription coregulator activity / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL
Similarity search - Function
Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / SH3 type barrels. - #30 / SH3 type barrels. - #140 / breast cancer carboxy-terminal domain / BRCT domain profile. ...Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / SH3 type barrels. - #30 / SH3 type barrels. - #140 / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / Ribosomal L40e family / BRCT domain superfamily / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / SH3 type barrels. / : / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eL40 fusion protein / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5047 Å
AuthorsWan, L. / Canny, M. / Juang, Y.C. / Durocher, D. / Sicheri, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
CIHR Foundation GrantFDN 143277 Canada
CitationJournal: To Be Published
Title: A genetically encoded inhibitor of 53BP1 to stimulate homology-based gene editing
Authors: Wan, L. / Canny, M. / Juang, Y.C. / Durocher, D. / Sicheri, F.
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Data collection
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Mar 6, 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

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Assembly

Deposited unit
B: Ubiquitin Variant i53
A: Tumor suppressor p53-binding protein 1


Theoretical massNumber of molelcules
Total (without water)21,8022
Polymers21,8022
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-8 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.531, 47.768, 94.237
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Ubiquitin Variant i53


Mass: 8531.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62987*PLUS
#2: Protein Tumor suppressor p53-binding protein 1 / p53BP1


Mass: 13270.034 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 (E. coli) / References: UniProt: Q12888
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.03 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium Cacodylate pH 6.0, 0.2 M Sodium Acetate, 27% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→24.593 Å / Num. obs: 6047 / % possible obs: 87.6 % / Redundancy: 1.75 % / Biso Wilson estimate: 38.374 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.46
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 1.16 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.75 / CC1/2: 0.782 / % possible all: 49.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692phasing
PHENIX1.9_1692refinement
XDSdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5047→24.593 Å / SU ML: 0.339773274872 / Cross valid method: FREE R-VALUE / σ(F): 1.367 / Phase error: 29.8859684112
RfactorNum. reflection% reflection
Rfree0.287 605 10.0049611378 %
Rwork0.231 5442 -
obs0.237 6047 92.5608449411 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.569184342 Å2
Refinement stepCycle: LAST / Resolution: 2.5047→24.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 0 1 1514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002450525976091540
X-RAY DIFFRACTIONf_angle_d0.7012962772142071
X-RAY DIFFRACTIONf_chiral_restr0.0227488722065231
X-RAY DIFFRACTIONf_plane_restr0.00216351605516263
X-RAY DIFFRACTIONf_dihedral_angle_d12.2785311199593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5047-2.75650.3195460618641140.2939411487481027X-RAY DIFFRACTION72.2609246358
2.7565-3.15470.389863752261580.2852465551181419X-RAY DIFFRACTION98.3167082294
3.1547-3.97180.29386754591630.2316303603031468X-RAY DIFFRACTION99.5118974985
3.9718-24.59440.2370220339521700.1961864292221528X-RAY DIFFRACTION99.2402104033
Refinement TLS params.Method: refined / Origin x: -11.5312456169 Å / Origin y: -8.76036296337 Å / Origin z: 11.5441735234 Å
111213212223313233
T0.172717895562 Å20.0060747512746 Å20.00847240452617 Å2-0.348194876435 Å2-0.0146929079452 Å2--0.239939694837 Å2
L1.75040465657 °20.463667267806 °2-0.396538446252 °2-4.26200296239 °2-0.773097938856 °2--2.09268817582 °2
S0.0580427581272 Å °-0.539703840605 Å °0.101716542311 Å °0.197032819738 Å °-0.0141882746276 Å °0.0538698022473 Å °-0.00418456791422 Å °-0.0108937211582 Å °-0.0508185156337 Å °
Refinement TLS groupSelection details: all

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