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Basic information

Entry
Database: PDB / ID: 1gzh
TitleCrystal structure of the BRCT domains of human 53BP1 bound to the p53 tumor supressor
Components
  • (CELLULAR TUMOR ANTIGEN ...) x 2
  • TUMOR SUPPRESSOR P53-BINDING PROTEIN 1
KeywordsGENE REGULATION / ANTI-ONCOGENE / DNA-BINDING / TRANSCRIPTION REGULATION / BCRT DOMAIN / APOPTOSIS / DISEASE MUTATION / ACTIVATOR / DNA- REPAIR
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 / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator ...ubiquitin-modified histone reader activity / positive regulation of isotype switching / histone H4K20me2 reader activity / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / mRNA transcription / positive regulation of programmed necrotic cell death / bone marrow development / DNA repair complex / circadian behavior / T cell proliferation involved in immune response / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / TP53 Regulates Transcription of Death Receptors and Ligands / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Activation of PUMA and translocation to mitochondria / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / thymocyte apoptotic process / telomeric DNA binding / B cell lineage commitment / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of reactive oxygen species metabolic process / rRNA transcription / Transcriptional Regulation by VENTX / positive regulation of execution phase of apoptosis / replicative senescence / general transcription initiation factor binding / cellular response to UV-C / cellular response to actinomycin D / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of RNA polymerase II transcription preinitiation complex assembly / histone reader activity / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / : / hematopoietic stem cell differentiation / Pyroptosis / viral process / embryonic organ development / chromosome organization / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / negative regulation of double-strand break repair via homologous recombination / somitogenesis / glial cell proliferation / hematopoietic progenitor cell differentiation / core promoter sequence-specific DNA binding / positive regulation of cardiac muscle cell apoptotic process / negative regulation of stem cell proliferation / cellular response to glucose starvation / cis-regulatory region sequence-specific DNA binding / mitophagy
Similarity search - Function
Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / BRCT domain / Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 ...Tumour suppressor p53-binding protein-1 Tudor domain / : / Tumour suppressor p53-binding protein-1 Tudor / BRCA1 C Terminus (BRCT) domain / : / : / BRCT domain / Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / breast cancer carboxy-terminal domain / p53-like transcription factor, DNA-binding / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ribosomal protein L2, domain 2 / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cellular tumor antigen p53 / TP53-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDerbyshire, D.J. / Doherty, A.J.
Citation
Journal: Embo J. / Year: 2002
Title: Crystal Structure of Human 53BP1 Brct Domains Bound to P53 Tumour Suppressor
Authors: Derbyshire, D.J. / Basu, B.P. / Serpell, L. / Joo, W. / Date, T. / Iwabuchi, K. / Doherty, A.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Purification, Crystallization and Preliminary X-Ray Analysis of the Brct Domains of Human 53BP1 Bound to the P53 Tumour Suppressor.
Authors: Derbyshire, D.J. / Basu, B.P. / Date, T. / Iwabuchi, K. / Doherty, A.J.
History
DepositionMay 22, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2002Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLULAR TUMOR ANTIGEN P53
B: TUMOR SUPPRESSOR P53-BINDING PROTEIN 1
C: CELLULAR TUMOR ANTIGEN P53
D: TUMOR SUPPRESSOR P53-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4128
Polymers101,0894
Non-polymers3234
Water1,982110
1
A: CELLULAR TUMOR ANTIGEN P53
B: TUMOR SUPPRESSOR P53-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7134
Polymers50,5512
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint0 kcal/mol
Surface area25120 Å2
MethodPQS
2
C: CELLULAR TUMOR ANTIGEN P53
D: TUMOR SUPPRESSOR P53-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6994
Polymers50,5372
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-0.7 kcal/mol
Surface area23890 Å2
MethodPQS
Unit cell
Length a, b, c (Å)71.520, 94.570, 136.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.85, 0.009, -0.527), (-0.017, 1, -0.01), (0.527, 0.017, 0.85)44.52079, -7.08252, -32.72585
2given(0.8, -0.052, -0.598), (0.035, 0.999, -0.04), (0.599, 0.011, 0.801)49.60453, -6.92727, -32.73009

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Components

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CELLULAR TUMOR ANTIGEN ... , 2 types, 2 molecules AC

#1: Protein CELLULAR TUMOR ANTIGEN P53 / TUMOR SUPPRESSOR P53 / PHOSPHOPROTEIN P53 / ANTIGEN NY-CO-13


Mass: 22375.479 Da / Num. of mol.: 1 / Fragment: DNA BINDING REGION, RESIDUES 95-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSET-B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: P04637
#3: Protein CELLULAR TUMOR ANTIGEN P53 / TUMOR SUPPRESSOR P53 / PHOSPHOPROTEIN P53 / ANTIGEN NY-CO-13


Mass: 22361.453 Da / Num. of mol.: 1 / Fragment: DNA BINDING REGION, RESIDUES 95-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSET-B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: P04637

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Protein , 1 types, 2 molecules BD

#2: Protein TUMOR SUPPRESSOR P53-BINDING PROTEIN 1 / P53-BINDING PROTEIN 1 / 53BP1


Mass: 28175.900 Da / Num. of mol.: 2 / Fragment: BRCT TANDEM REPEAT, RESIDUES 1724-1972
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSET-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: Q12888

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Non-polymers , 3 types, 114 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.13 Å3/Da / Density % sol: 41.76 %
Description: STRUCTURE DETERMINATION COMPLETED BY MOLECULAR REPLACEMENT WITH PDB ENTRY 1KZY (VIA PERSONAL COMMUNICATION)
Crystal growpH: 7.4
Details: 50 MM TRIS PH 7.4, 250 MM AMMONIUM SULFATE, 25% POLYETHYLENE GLYCOL 4000
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein11
250 mMTris-HCl11pH7.4
420-25 %PEG400011
3ammonium sulfate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→38.84 Å / Num. obs: 54119 / % possible obs: 99.1 % / Redundancy: 7.7 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 6.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 1.4 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 55 Å
Reflection shell
*PLUS
% possible obs: 96.9 % / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TSR

1tsr


Resolution: 2.6→38.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1861614.03 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CHAIN A HAS BREAKS BETWEEN RESIDUES 183-188 AND 224-227. DISORDER IS ALSO EVIDENT FOR RESIDUE 200. CHAIN B IS UNINTREPRETABLE BETWEEN RESIDUES 1750-1768. CHAIN C HAS NO BREAKS BUT ONLY ...Details: CHAIN A HAS BREAKS BETWEEN RESIDUES 183-188 AND 224-227. DISORDER IS ALSO EVIDENT FOR RESIDUE 200. CHAIN B IS UNINTREPRETABLE BETWEEN RESIDUES 1750-1768. CHAIN C HAS NO BREAKS BUT ONLY EXTENDS FROM 95-289. CHAIN D HAS A BREAK BETWEEN 1740-1768 AND 1794-1796, AND ONLY EXTENDS FROM 1725-1969.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2835 5.2 %RANDOM
Rwork0.238 ---
obs0.238 54119 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.1016 Å2 / ksol: 0.340415 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-9.17 Å20 Å20 Å2
2---14.42 Å20 Å2
3---5.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6508 0 12 110 6630
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.7862
X-RAY DIFFRACTIONc_mcangle_it2.9313
X-RAY DIFFRACTIONc_scbond_it2.4462.5
X-RAY DIFFRACTIONc_scangle_it3.6383.5
Refine LS restraints NCSRms dev Biso : 15 Å2 / Rms dev position: 1.99 Å / Weight Biso : 2 / Weight position: 300
LS refinement shellResolution: 2.6→2.62 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.34 58 5.4 %
Rwork0.348 1023 -
obs--95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.PARAM
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 500 Å / % reflection Rfree: 5.2 % / Rfactor Rfree: 0.2883 / Rfactor Rwork: 0.2381
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00782
X-RAY DIFFRACTIONc_angle_deg1.3485
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
LS refinement shell
*PLUS
Rfactor Rfree: 0.34

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