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- PDB-2wgx: HUMAN P53 CORE DOMAIN MUTANT M133L-V203A-Y236F-N239Y-T253I-N268D -

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Basic information

Entry
Database: PDB / ID: 2wgx
TitleHUMAN P53 CORE DOMAIN MUTANT M133L-V203A-Y236F-N239Y-T253I-N268D
ComponentsCELLULAR TUMOR ANTIGEN P53
KeywordsCELL CYCLE / P53 / P63 / P73 / CANCER / NUCLEUS / APOPTOSIS / TUMOR SUPPRESSOR / SECOND-SITE SUPPRESSOR MUTATION / DNA-BINDING DOMAIN / TRANSCRIPTION REGULATION / NUCLEAR PROTEIN / PROTEIN STABILIZATION / LI-FRAUMENI SYNDROME / METAL BINDING / ZINC / SUPERSTABLE MUTANT / DNA-BINDING PROTEIN / POLYMORPHISM
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 / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / circadian behavior / bone marrow development / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / negative regulation of DNA replication / 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 / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of release of cytochrome c from mitochondria / necroptotic process / Zygotic genome activation (ZGA) / positive regulation of execution phase of apoptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / replicative senescence / response to X-ray / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / mitophagy / cellular response to UV-C / positive regulation of RNA polymerase II transcription preinitiation complex assembly / hematopoietic stem cell differentiation / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chromosome organization / T cell proliferation involved in immune response / Pyroptosis / embryonic organ development / glial cell proliferation / viral process / cis-regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / hematopoietic progenitor cell differentiation / type II interferon-mediated signaling pathway / somitogenesis / cellular response to actinomycin D / core promoter sequence-specific DNA binding / cellular response to glucose starvation / negative regulation of stem cell proliferation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / response to salt stress / cardiac muscle cell apoptotic process / mitotic G1 DNA damage checkpoint signaling / tumor necrosis factor-mediated signaling pathway / 14-3-3 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
Cellular tumor antigen p53
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJoerger, A.C. / Khoo, K.H. / Fersht, A.R.
Citation
Journal: Protein Eng.Des.Sel. / Year: 2009
Title: Stabilising the DNA-Binding Domain of P53 by Rational Design of its Hydrophobic Core.
Authors: Khoo, K.H. / Joerger, A.C. / Freund, S.M.V. / Fersht, A.R.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of a Superstable Mutant of Human P53 Core Domain. Insights Into the Mechanism of Rescuing Oncogenic Mutations.
Authors: Joerger, A.C. / Allen, M.D. / Fersht, A.R.
History
DepositionApr 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3054
Polymers49,1742
Non-polymers1312
Water8,197455
1
A: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6522
Polymers24,5871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6522
Polymers24,5871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.328, 71.075, 104.915
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 24586.896 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 94-312 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04637
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 133 TO LEU ENGINEERED RESIDUE IN CHAIN A, VAL 203 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, MET 133 TO LEU ENGINEERED RESIDUE IN CHAIN A, VAL 203 TO ALA ENGINEERED RESIDUE IN CHAIN A, TYR 236 TO PHE ENGINEERED RESIDUE IN CHAIN A, ASN 239 TO TYR ENGINEERED RESIDUE IN CHAIN A, THR 253 TO ILE ENGINEERED RESIDUE IN CHAIN A, ASN 268 TO ASP ENGINEERED RESIDUE IN CHAIN B, MET 133 TO LEU ENGINEERED RESIDUE IN CHAIN B, VAL 203 TO ALA ENGINEERED RESIDUE IN CHAIN B, TYR 236 TO PHE ENGINEERED RESIDUE IN CHAIN B, ASN 239 TO TYR ENGINEERED RESIDUE IN CHAIN B, THR 253 TO ILE ENGINEERED RESIDUE IN CHAIN B, ASN 268 TO ASP
Sequence detailsENGINEERED MUTATIONS

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: SITTING DROP VAPOR DIFFUSION AT 21 DEGREE C. PROTEIN SOLUTION: 6 MG/ML IN 25 MM SODIUM PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM HEPES PH 7.2, 19 % PEG 4000, 5 MM DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.75→65.4 Å / Num. obs: 48639 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 13.61 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.5 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UOL

1uol


Resolution: 1.75→24.607 Å / SU ML: 0.17 / σ(F): 1.44 / Phase error: 20.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1986 2428 5 %
Rwork0.1695 --
obs0.171 48562 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.771 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso mean: 17.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.0011 Å20 Å20 Å2
2---3.2818 Å20 Å2
3----1.8244 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 2 455 3525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083176
X-RAY DIFFRACTIONf_angle_d1.1784312
X-RAY DIFFRACTIONf_dihedral_angle_d14.8451196
X-RAY DIFFRACTIONf_chiral_restr0.083472
X-RAY DIFFRACTIONf_plane_restr0.006570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.22941290.2032438X-RAY DIFFRACTION81
1.7699-1.79070.2161700.19142593X-RAY DIFFRACTION88
1.7907-1.81250.21351410.18182822X-RAY DIFFRACTION92
1.8125-1.83550.20691640.17232732X-RAY DIFFRACTION92
1.8355-1.85960.2411510.1752779X-RAY DIFFRACTION92
1.8596-1.88510.22441400.17192795X-RAY DIFFRACTION93
1.8851-1.9120.24091570.17432829X-RAY DIFFRACTION94
1.912-1.94050.19681510.16422817X-RAY DIFFRACTION93
1.9405-1.97080.1731270.16552872X-RAY DIFFRACTION94
1.9708-2.00310.17861510.17182813X-RAY DIFFRACTION95
2.0031-2.03770.24951480.16492880X-RAY DIFFRACTION95
2.0377-2.07470.20421660.16562855X-RAY DIFFRACTION96
2.0747-2.11460.21921400.16482897X-RAY DIFFRACTION96
2.1146-2.15770.20291660.15992892X-RAY DIFFRACTION96
2.1577-2.20460.20191290.15592942X-RAY DIFFRACTION97
2.2046-2.25580.17791730.15932922X-RAY DIFFRACTION97
2.2558-2.31220.2111360.15442950X-RAY DIFFRACTION98
2.3122-2.37470.16981590.16172959X-RAY DIFFRACTION98
2.3747-2.44450.15571510.15143008X-RAY DIFFRACTION99
2.4445-2.52330.18391570.15182992X-RAY DIFFRACTION99
2.5233-2.61340.17831290.16643026X-RAY DIFFRACTION99
2.6134-2.71790.21661430.16063005X-RAY DIFFRACTION100
2.7179-2.84150.22111530.17643035X-RAY DIFFRACTION100
2.8415-2.9910.21261650.17972978X-RAY DIFFRACTION100
2.991-3.17810.17641360.17283017X-RAY DIFFRACTION100
3.1781-3.42280.16841540.16283032X-RAY DIFFRACTION100
3.4228-3.76620.1631580.15872984X-RAY DIFFRACTION100
3.7662-4.30870.15791760.15112974X-RAY DIFFRACTION99
4.3087-5.41890.18121680.14612975X-RAY DIFFRACTION99
5.4189-24.60920.23771530.18762911X-RAY DIFFRACTION96

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