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- PDB-4ibw: Human p53 core domain with hot spot mutation R273H and second-sit... -

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Basic information

Entry
Database: PDB / ID: 4ibw
TitleHuman p53 core domain with hot spot mutation R273H and second-site suppressor mutation T284R in sequence-specific complex with DNA
Components
  • Cellular tumor antigen p53P53
  • 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 / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing 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 / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / 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 neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / chromosome organization / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / MDM2/MDM4 family protein binding / glial cell proliferation / embryonic organ development / cellular response to glucose starvation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / cardiac muscle cell apoptotic process / response to salt stress / transcription initiation-coupled chromatin remodeling / mitotic G1 DNA damage checkpoint signaling / 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: 1.791 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)27,32820
Polymers26,2072
Non-polymers1,12118
Water6,035335
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)54,65540
Polymers52,4144
Non-polymers2,24136
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Unit cell
Length a, b, c (Å)137.562, 49.923, 34.239
Angle α, β, γ (deg.)90.000, 93.680, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cellular tumor antigen p53 / P53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 22542.625 Da / Num. of mol.: 1 / Fragment: DNA binding domain / Mutation: R273H, T284R
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 45.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 1:2.4 PROTEIN/DNA RATIO, 14% PEG 3350, 0.14M 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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 25, 2008 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.79→40 Å / Num. obs: 21929 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.117 / Χ2: 1.065 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.79-1.827.20.53610720.8991100
1.82-1.857.20.52510680.961100
1.85-1.897.20.4510990.9861100
1.89-1.937.30.410951.0381100
1.93-1.977.30.33310971.0661100
1.97-2.027.40.30411201.0871100
2.02-2.077.40.2610571.0741100
2.07-2.127.40.23910751.1561100
2.12-2.187.50.20910981.1011100
2.18-2.267.50.18211031.1351100
2.26-2.347.50.16610721.1011100
2.34-2.437.50.15711141.1041100
2.43-2.547.50.13910891.1711100
2.54-2.677.50.12510941.1481100
2.67-2.847.50.10611131.1141100
2.84-3.067.50.08410901.0611100
3.06-3.377.40.06210971.0341100
3.37-3.867.40.0511181.0141100
3.86-4.867.20.04711151.0341100
4.86-406.90.04711430.9951100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AC0, chain A

2ac0


Resolution: 1.791→34.32 Å / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.8942 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / Phase error: 17.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1876 1114 5.08 %RANDOM
Rwork0.1417 ---
obs0.1441 21923 99.84 %-
all-21923 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.22 Å2 / Biso mean: 16.1195 Å2 / Biso min: 2.16 Å2
Refinement stepCycle: LAST / Resolution: 1.791→34.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 225 69 335 2172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062009
X-RAY DIFFRACTIONf_angle_d1.1462742
X-RAY DIFFRACTIONf_chiral_restr0.078290
X-RAY DIFFRACTIONf_plane_restr0.005324
X-RAY DIFFRACTIONf_dihedral_angle_d17.027792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.791-1.87220.23891470.17782527267499
1.8722-1.97090.21361180.160726122730100
1.9709-2.09430.21321360.148525722708100
2.0943-2.2560.18521340.139826212755100
2.256-2.4830.20191470.146325832730100
2.483-2.84210.1931350.144626162751100
2.8421-3.58020.18891270.128326302757100
3.5802-34.32590.1551700.131626482818100
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)
11.220.2121-0.47560.8229-0.26830.6534-0.03520.22610.2002-0.21450.09290.0997-0.04990.0786-0.01510.09540.0006-0.02670.1466-0.01170.0932-30.0363-2.721-21.441
24.56343.57961.48372.83871.01141.08540.1814-0.58260.56290.2076-0.36240.30670.034-0.07250.14980.0991-0.05830.00870.1616-0.03990.1375-17.505911.8097-3.7556
31.85341.3182-0.39421.886-0.36110.05050.0163-0.15090.07750.004-0.04840.03690.00160.01050.03120.07050.001-0.00660.0735-0.02210.0305-24.51542.9743-8.8479
42.96080.1778-0.65270.90860.49231.5501-0.07510.1495-0.1215-0.1047-0.0237-0.05220.00720.04110.06820.0817-0.0042-0.00490.0257-0.01160.0464-15.9853-4.2583-21.9719
53.64622.3322-0.36224.1306-0.1242.6364-0.0006-0.4429-0.7820.22720.0422-0.31650.1060.33430.04620.10460.03530.00030.13750.04190.1316-6.6251-10.1728-11.309
61.32820.32790.08330.2120.45441.76530.3848-0.5505-0.25230.3822-0.0968-0.11260.1689-0.0030.08140.1418-0.07890.00140.23490.0881-0.0161-20.0431-10.5871-4.5239
70.55420.03110.92952.5820.98071.93960.05040.0078-0.1112-0.05620.07190.03950.441-0.1483-0.03850.1037-0.01970.00320.06960.00150.076-18.922-16.1262-19.8686
80.82870.28970.10661.3671-0.23111.0787-0.0062-0.44060.09070.2826-0.03450.1932-0.0415-0.02670.01110.117-0.00730.02930.1412-0.03110.0704-30.9701-5.8228-3.9116
91.91120.58170.03631.09390.00960.4934-0.0320.0140.0484-0.00340.02320.050.01430.01840.01890.0638-0.0026-0.0020.04060.00270.0367-19.0816-1.0869-15.1715
105.2517-2.00245.82243.938-4.62538.5898-0.10460.27420.35970.0446-0.1034-0.0465-0.18290.19920.20390.0754-0.01180.00390.0816-0.0090.1288-14.911218.6759-15.7868
112.52120.3651-1.75132.4322-0.04491.57420.110.01420.13230.08070.1311-0.0062-0.13370.016-0.11090.0630.0026-0.01650.0707-0.02750.09942.128614.8094-18.3892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 94:112 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 113:123 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 124:155 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 156:176 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 177:194 )A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 195:203 )A0
7X-RAY DIFFRACTION7CHAIN A AND (RESID 204:213 )A0
8X-RAY DIFFRACTION8CHAIN A AND (RESID 214:229 )A0
9X-RAY DIFFRACTION9CHAIN A AND (RESID 230:277 )A0
10X-RAY DIFFRACTION10CHAIN A AND (RESID 278:293 )A0
11X-RAY DIFFRACTION11CHAIN B AND (RESID 1:12 )B0

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