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- PDB-2ybg: Structure of Lys120-acetylated p53 core domain -

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Basic information

Entry
Database: PDB / ID: 2ybg
TitleStructure of Lys120-acetylated p53 core domain
ComponentsCELLULAR TUMOR ANTIGEN P53
KeywordsCELL CYCLE / TUMOR SUPPRESSOR / CANCER / LYSINE ACETYLATION / APOPTOSIS
Function / homology
Function and homology information


negative regulation of helicase 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 / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...negative regulation of helicase 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 / 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 / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / mRNA transcription / positive regulation of programmed necrotic cell death / bone marrow development / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / TP53 Regulates Transcription of Death Receptors and Ligands / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / Activation of PUMA and translocation to mitochondria / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / thymocyte apoptotic process / B cell lineage commitment / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / 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 / negative regulation of reactive oxygen species metabolic process / rRNA transcription / Transcriptional Regulation by VENTX / positive regulation of execution phase of apoptosis / replicative senescence / general transcription initiation factor binding / cellular response to UV-C / cellular response to actinomycin D / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / hematopoietic stem cell differentiation / Pyroptosis / viral process / embryonic organ development / chromosome organization / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / glial cell proliferation / hematopoietic progenitor cell differentiation / core promoter sequence-specific DNA binding / positive regulation of cardiac muscle cell apoptotic process / negative regulation of stem cell proliferation / cellular response to glucose starvation / cis-regulatory region sequence-specific DNA binding / mitophagy / negative regulation of fibroblast proliferation / positive regulation of intrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / Regulation of TP53 Activity through Acetylation / gastrulation / mitotic G1 DNA damage checkpoint signaling / response to salt stress / 14-3-3 protein binding / negative regulation of proteolysis / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription repressor complex
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: 1.9 Å
AuthorsArbely, E. / Allen, M.D. / Joerger, A.C. / Fersht, A.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Acetylation of Lysine 120 of P53 Endows DNA- Binding Specificity at Effective Physiological Salt Concentration.
Authors: Arbely, E. / Natan, E. / Brandt, T. / Allen, M.D. / Veprintsev, D.B. / Robinson, C.V. / Chin, J.W. / Joerger, A.C. / Fersht, A.R.
History
DepositionMar 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
C: CELLULAR TUMOR ANTIGEN P53
D: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4488
Polymers90,1864
Non-polymers2624
Water11,602644
1
A: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6122
Polymers22,5471
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)22,6122
Polymers22,5471
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6122
Polymers22,5471
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CELLULAR TUMOR ANTIGEN P53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6122
Polymers22,5471
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.926, 69.581, 83.494
Angle α, β, γ (deg.)90.00, 90.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 22546.611 Da / Num. of mol.: 4 / Fragment: DNA-BINDING DOMAIN, RESIDUES 94-293
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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: PROTEIN SOLUTION: 5 MG/ML PROTEIN IN 20 MM CITRATE BUFFER PH 6.1, 150 MM NACL, 10 MM DTT. CRYSTALLIZATION BUFFER: 26% (W/V) PEG 3350, 43 MM SODIUM ACETATE AND 100 MM HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.179
ReflectionResolution: 1.9→49 Å / Num. obs: 60047 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.4 / % possible all: 98.8

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.212 Å / σ(F): 1.35 / Phase error: 34.69 / Stereochemistry target values: TWIN_LSQ_F
Details: IN THE UNBOUND P53 DNA-BINDING DOMAIN, THE LYS120 SIDE CHAIN IS HIGHLY FLEXIBLE. SIMILARLY, THE SIDE CHAIN OF ACETYLATED LYS120 SHOWED A HIGH DEGREE OF FLEXIBILITY, AND THE LACK OF DEFINED ...Details: IN THE UNBOUND P53 DNA-BINDING DOMAIN, THE LYS120 SIDE CHAIN IS HIGHLY FLEXIBLE. SIMILARLY, THE SIDE CHAIN OF ACETYLATED LYS120 SHOWED A HIGH DEGREE OF FLEXIBILITY, AND THE LACK OF DEFINED ELECTRON DENSITY PREVENTED UNAMBIGUOUS MODELING OF THE ACETYLATED SIDE CHAIN.
RfactorNum. reflection% reflection
Rfree0.226 6156 6 %
Rwork0.1744 --
obs0.1768 101869 83.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.326 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.1068 Å20 Å2-2.0096 Å2
2--11.937 Å20 Å2
3----5.8302 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 4 644 6704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066221
X-RAY DIFFRACTIONf_angle_d0.978451
X-RAY DIFFRACTIONf_dihedral_angle_d15.912327
X-RAY DIFFRACTIONf_chiral_restr0.064924
X-RAY DIFFRACTIONf_plane_restr0.0041122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.93280.31842200.26074823X-RAY DIFFRACTION79
1.9328-1.9680.27982590.25694771X-RAY DIFFRACTION78
1.968-2.00580.29692540.24394824X-RAY DIFFRACTION79
2.0058-2.04670.28862670.2314864X-RAY DIFFRACTION78
2.0467-2.09120.25812880.22054725X-RAY DIFFRACTION78
2.0912-2.13990.26562740.21774790X-RAY DIFFRACTION79
2.1399-2.19340.26172550.20984804X-RAY DIFFRACTION79
2.1934-2.25270.23712270.20734896X-RAY DIFFRACTION79
2.2527-2.31890.25942300.20384910X-RAY DIFFRACTION80
2.3189-2.39380.26822380.19254826X-RAY DIFFRACTION80
2.3938-2.47930.23622750.19734848X-RAY DIFFRACTION79
2.4793-2.57850.27362430.19384914X-RAY DIFFRACTION80
2.5785-2.69580.2312440.18594809X-RAY DIFFRACTION80
2.6958-2.83790.24892880.18294828X-RAY DIFFRACTION79
2.8379-3.01550.20152130.16634931X-RAY DIFFRACTION80
3.0155-3.24820.21192680.1574848X-RAY DIFFRACTION79
3.2482-3.57460.20652500.13424855X-RAY DIFFRACTION80
3.5746-4.0910.17072820.12794787X-RAY DIFFRACTION78
4.091-5.15080.17762290.11974566X-RAY DIFFRACTION75
5.1508-32.11850.20382960.15425138X-RAY DIFFRACTION84

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