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- PDB-4lof: Human p53 Core Domain Mutant V157F/N235K/N239Y -

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Basic information

Entry
Database: PDB / ID: 4lof
TitleHuman p53 Core Domain Mutant V157F/N235K/N239Y
ComponentsCellular tumor antigen p53
KeywordsAPOPTOSIS / Beta Sandwich / Tumor Suppressor / DNA Binding / Nuclear
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 / hematopoietic progenitor cell differentiation / Association of TriC/CCT with target proteins during biosynthesis / 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 / Transcriptional Regulation by VENTX / TFIID-class transcription factor complex binding / replicative senescence / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / determination of adult lifespan / 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 / response to gamma radiation / 14-3-3 protein binding / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / DNA damage response, signal transduction by p53 class mediator / protein phosphatase 2A binding / 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 / promoter-specific chromatin binding / Stabilization of p53 / molecular condensate scaffold activity / negative regulation of cell growth / nucleotide-excision repair / G2/M Checkpoints / receptor tyrosine kinase binding / Autodegradation of the E3 ubiquitin ligase COP1 / cellular senescence / PML body / positive regulation of miRNA transcription / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / PKR-mediated signaling / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / transcription coactivator binding / positive regulation of reactive oxygen species metabolic process / intracellular protein localization / 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: 2 Å
AuthorsWallentine, B.D. / Wang, Y. / Luecke, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue.
Authors: Wallentine, B.D. / Wang, Y. / Tretyachenko-Ladokhina, V. / Tan, M. / Senear, D.F. / Luecke, H.
History
DepositionJul 12, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionJul 31, 2013ID: 2QVQ
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7642
Polymers24,6991
Non-polymers651
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.268, 51.128, 33.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

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Components

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


Mass: 24699.070 Da / Num. of mol.: 1 / Fragment: p53 Core Domain (UNP residues 94-312) / Mutation: V157F, N235K, N239Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P53, TP53 / Plasmid: Pse420 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04637
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.88 Å3/Da / Density % sol: 34.47 %
Crystal growMethod: vapor diffusion / pH: 7.6
Details: 2 microliters protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliters reservoir buffer with 200 mM di-sodium hydrogen ...Details: 2 microliters protein solution (around 5.0-7.0 mg/ml protein in 20 mM Tris pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 microliters reservoir buffer with 200 mM di-sodium hydrogen phosphate dehydrate (Na2HPO4), 20% (w/v) PEG 3350, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.5418
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2005
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→46.154 Å / Num. all: 12861 / Num. obs: 12861 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rsym value: 0.169 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
CNSrefinement
Blu-Icedata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2OCJ (Chain A)

2ocj


Resolution: 2→46.15 Å / SU ML: 0.31 / σ(F): 1.39 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1026 8 %Random
Rwork0.1912 ---
obs0.1964 12818 97.22 %-
all-12818 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.24 Å2
Refinement stepCycle: LAST / Resolution: 2→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 1 134 1699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081601
X-RAY DIFFRACTIONf_angle_d1.1232167
X-RAY DIFFRACTIONf_dihedral_angle_d12.721611
X-RAY DIFFRACTIONf_chiral_restr0.077233
X-RAY DIFFRACTIONf_plane_restr0.005285
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10550.36721460.28551680X-RAY DIFFRACTION99
2.1055-2.23740.32481470.2431680X-RAY DIFFRACTION99
2.2374-2.41010.2491440.21631663X-RAY DIFFRACTION98
2.4101-2.65260.26661470.20891686X-RAY DIFFRACTION98
2.6526-3.03640.28141460.2131690X-RAY DIFFRACTION98
3.0364-3.82530.2921450.16421653X-RAY DIFFRACTION95
3.8253-46.16590.18021510.15321740X-RAY DIFFRACTION94
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)
13.72-0.11850.81641.8032-0.4150.6813-0.0543-0.19650.45570.103-0.0578-0.2061-0.08020.06290.09380.2002-0.01260.00230.1392-0.03320.174219.63987.930710.4404
23.4553-0.2098-0.22814.2408-0.95114.1526-0.08540.0631-0.2267-0.10930.10710.02460.1728-0.10350.05810.1082-0.0212-0.05170.1588-0.04180.183515.2518-6.71515.8404
38.14391.07941.01764.9005-3.39095.42310.28870.5721-0.4292-0.20640.59130.4367-0.1202-1.2834-0.57650.28160.0125-0.01910.23980.05770.2226.2809-4.97530.754
43.51991.61861.11474.7532-1.49092.2666-0.0092-1.22320.57471.55420.108-0.34480.15510.1019-0.07810.37170.0124-0.0460.395-0.18780.39468.88797.984417.6401
54.339-3.2223-1.54114.67460.30721.19360.07860.0923-0.1244-0.0762-0.09930.0746-0.02020.08540.02760.1719-0.0359-0.02730.1474-0.0220.145219.02020.2346.0595
63.55311.7689-4.68252.7801-4.08047.7845-0.0332-0.58550.21680.0509-0.5709-1.0425-0.07740.83920.42170.2940.0238-0.04280.26770.01830.345838.97954.69318.2865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 94:155)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 156:203)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 204:213)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 214:229)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 230:277)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 278:291)

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