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- PDB-4ibv: Human p53 core domain with hot spot mutation R273C and second-sit... -

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Basic information

Entry
Database: PDB / ID: 4ibv
TitleHuman p53 core domain with hot spot mutation R273C and second-site suppressor mutation S240R in sequence-specific complex with DNA
Components
  • Cellular tumor antigen p53
  • DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA / METAL-BINDING / LOOP-SHEET-HELIX MOTIF / TRANSCRIPTION / ACTIVATOR / ANTI-ONCOGENE / APOPTOSIS / CELL CYCLE / DISEASE MUTATION / RESCUE MUTATION / TUMOR SUPPRESSOR / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


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 ...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 / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oligodendrocyte apoptotic process / negative regulation of miRNA processing / negative regulation of helicase activity / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / positive regulation of programmed necrotic cell death / negative regulation of mitophagy / mRNA transcription / circadian behavior / bone marrow development / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / regulation of DNA damage response, signal transduction by p53 class mediator / RUNX3 regulates CDKN1A transcription / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / : / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / ER overload response / B cell lineage commitment / thymocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of DNA replication / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / negative regulation of telomere maintenance via telomerase / necroptotic process / positive regulation of release of cytochrome c from mitochondria / Zygotic genome activation (ZGA) / Association of TriC/CCT with target proteins during biosynthesis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of execution phase of apoptosis / T cell proliferation involved in immune response / TFIID-class transcription factor complex binding / rRNA transcription / 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 / Transcriptional Regulation by VENTX / general transcription initiation factor binding / cellular response to actinomycin D / replicative senescence / response to X-ray / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to UV-C / neuroblast proliferation / hematopoietic stem cell differentiation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / mitophagy / chromosome organization / Pyroptosis / viral process / embryonic organ development / cis-regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / type II interferon-mediated signaling pathway / glial cell proliferation / somitogenesis / hematopoietic progenitor cell differentiation / : / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / cellular response to glucose starvation / positive regulation of cardiac muscle cell apoptotic process / negative regulation of fibroblast proliferation / response to salt stress / mitotic G1 DNA damage checkpoint signaling / tumor necrosis factor-mediated signaling pathway / cardiac muscle cell apoptotic process / gastrulation / MDM2/MDM4 family protein binding / Regulation of TP53 Activity through Acetylation
Similarity search - Function
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 ...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 / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsEldar, A. / Rozenberg, H. / Diskin-Posner, Y. / Shakked, Z.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions.
Authors: Eldar, A. / Rozenberg, H. / Diskin-Posner, Y. / Rohs, R. / Shakked, Z.
History
DepositionDec 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,68610
Polymers26,1862
Non-polymers5008
Water2,954164
1
A: Cellular tumor antigen p53
B: DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3')
hetero molecules

A: Cellular tumor antigen p53
B: DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,37220
Polymers52,3724
Non-polymers1,00016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5450 Å2
ΔGint-10 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.631, 50.302, 34.008
Angle α, β, γ (deg.)90.00, 93.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cellular tumor antigen p53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 22521.646 Da / Num. of mol.: 1 / Fragment: DNA binding domain / Mutation: R273C, S240R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P53, TP53 / Plasmid: pET-27-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04637
#2: DNA chain DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3')


Mass: 3664.380 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 1:2.4 PROTEIN/DNA RATIO, 16% PEG 3350, 0.18M NH4F, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2009 / Details: Pt coated Si mirror in Kirkpatrick-Baez geometry
RadiationMonochromator: SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 13264 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.143.30.255183.6
2.14-2.183.70.251188.7
2.18-2.224.10.213190.1
2.22-2.264.30.209192.7
2.26-2.314.70.21195.2
2.31-2.3750.191197
2.37-2.425.30.19196.6
2.42-2.495.80.182198
2.49-2.5660.163198.6
2.56-2.656.40.157198.6
2.65-2.746.70.145198.8
2.74-2.857.10.134198.6
2.85-2.987.50.123199.1
2.98-3.147.60.105199
3.14-3.337.70.08199.3
3.33-3.597.70.065199.1
3.59-3.957.70.058199.3
3.95-4.527.60.053199.4
4.52-5.77.60.05199.6
5.7-507.30.045199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_1405refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AC0, chain A

2ac0


Resolution: 2.1→47.235 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 24.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 667 5.03 %
Rwork0.1614 --
obs0.1648 13262 96.25 %
all-13262 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.025 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1535 221 29 164 1949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071947
X-RAY DIFFRACTIONf_angle_d1.212674
X-RAY DIFFRACTIONf_dihedral_angle_d18.445771
X-RAY DIFFRACTIONf_chiral_restr0.078284
X-RAY DIFFRACTIONf_plane_restr0.006315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.2580.24161010.18082293X-RAY DIFFRACTION87
2.258-2.48520.25811560.17862460X-RAY DIFFRACTION97
2.4852-2.84480.25521430.18392581X-RAY DIFFRACTION99
2.8448-3.58390.22531380.16042591X-RAY DIFFRACTION99
3.5839-47.24720.20311290.14152670X-RAY DIFFRACTION99
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)
12.9767-1.37510.55262.2381-0.06150.82-0.11870.10880.43070.1479-0.1087-0.5258-0.1170.00830.15850.1446-0.0215-0.04820.11110.04020.195124.376725.6079-2.3676
25.3704-4.0558-1.64585.5512-0.0732.44-0.12240.5668-1.1194-0.1411-0.0810.53870.185-0.57480.32730.2177-0.05330.03650.2567-0.05130.27.437814.6569-5.0018
33.5249-1.48211.07693.2864-0.04911.9552-0.02250.24020.04140.0028-0.1132-0.19620.02740.04360.08940.10510.00340.01890.09860.0190.059822.135819.3778-4.4248
47.62061.66812.59553.54044.36425.99270.0419-0.59070.9941-0.1285-0.1361-0.0898-0.4998-0.36050.12350.29270.0154-0.08880.13740.02030.411916.207244.0953-1.2346
50.36160.08380.2190.12981.21456.5309-0.00480.04340.07510.10970.1589-0.03770.11310.1951-0.16590.26240.01750.00050.25870.04060.1554-1.540.17170.5263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 94:176)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 177:194)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 195:277)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 278:293)
5X-RAY DIFFRACTION5CHAIN B AND (RESID 1:11)

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