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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


negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity ...negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / oligodendrocyte apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / cellular response to actinomycin D / circadian behavior / positive regulation of programmed necrotic cell death / RUNX3 regulates CDKN1A transcription / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / Regulation of TP53 Activity through Association with Co-factors / Urea cycle / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / intrinsic apoptotic signaling pathway by p53 class mediator / entrainment of circadian clock by photoperiod / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / hematopoietic progenitor cell differentiation / negative regulation of telomere maintenance via telomerase / 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 in response to DNA damage by p53 class mediator / replicative senescence / Transcriptional Regulation by VENTX / TFIID-class transcription factor complex binding / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / determination of adult lifespan / Pyroptosis / positive regulation of RNA polymerase II transcription preinitiation complex assembly / general transcription initiation factor binding / negative regulation of fibroblast proliferation / positive regulation of execution phase of apoptosis / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to glucose starvation / core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway / 14-3-3 protein binding / response to gamma radiation / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / DNA damage response, signal transduction by p53 class mediator / transcription initiation-coupled chromatin remodeling / molecular function activator activity / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / cellular response to xenobiotic stimulus / TP53 Regulates Metabolic Genes / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / Regulation of NF-kappa B signaling / mRNA 3'-UTR binding / protein tetramerization / molecular condensate scaffold activity / promoter-specific chromatin binding / Stabilization of p53 / negative regulation of cell growth / nucleotide-excision repair / G2/M Checkpoints / receptor tyrosine kinase binding / Autodegradation of the E3 ubiquitin ligase COP1 / PML body / cellular senescence / PKR-mediated signaling / positive regulation of miRNA transcription / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / intracellular protein localization / transcription coactivator binding / positive regulation of reactive oxygen species metabolic process / histone deacetylase binding
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 ...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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