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- PDB-2ocj: Human p53 core domain in the absence of DNA -

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Basic information

Entry
Database: PDB / ID: 2ocj
TitleHuman p53 core domain in the absence of DNA
ComponentsP53 TUMOR SUPPRESSOR
KeywordsDNA BINDING PROTEIN / TUMOR SUPPRESSOR / P53 / CANCER / TETRAMER
Function / homology
Function and homology information


negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of glucose catabolic process to lactate via pyruvate / regulation of fibroblast apoptotic process / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 helicase activity / signal transduction by p53 class mediator / negative regulation of glucose catabolic process to lactate via pyruvate / regulation of fibroblast apoptotic process / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / : / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / germ cell nucleus / regulation of tissue remodeling / ATP-dependent DNA/DNA annealing activity / thymocyte apoptotic process / oligodendrocyte apoptotic process / oxidative stress-induced premature senescence / positive regulation of mitochondrial membrane permeability / positive regulation of thymocyte apoptotic process / bone marrow development / cellular response to actinomycin D / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / circadian behavior / T cell lineage commitment / positive regulation of programmed necrotic cell death / T cell proliferation involved in immune response / B cell lineage commitment / 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 / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / regulation of DNA damage response, signal transduction by p53 class mediator / Regulation of TP53 Activity through Association with Co-factors / ER overload response / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / neuroblast proliferation / cardiac septum morphogenesis / necroptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / negative regulation of DNA replication / hematopoietic stem cell differentiation / negative regulation of mitophagy / Zygotic genome activation (ZGA) / somitogenesis / 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 / intrinsic apoptotic signaling pathway by p53 class mediator / 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 / rRNA transcription / negative regulation of reactive oxygen species metabolic process / replicative senescence / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / TFIID-class transcription factor complex binding / Transcriptional Regulation by VENTX / cellular response to UV-C / hematopoietic progenitor cell differentiation / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / embryonic organ development / chromosome organization / Pyroptosis / positive regulation of RNA polymerase II transcription preinitiation complex assembly / general transcription initiation factor binding / response to X-ray / positive regulation of execution phase of apoptosis / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / glial cell proliferation / cellular response to glucose starvation / core promoter sequence-specific DNA binding / mitophagy / multicellular organism growth / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / determination of adult lifespan / transcription repressor complex / stem cell proliferation / fibroblast proliferation / response to salt stress / negative regulation of proteolysis / mitotic G1 DNA damage checkpoint signaling / gastrulation / positive regulation of intrinsic apoptotic signaling pathway / reactive oxygen species metabolic process
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: 2.05 Å
AuthorsWang, Y. / Rosengarth, A. / Luecke, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of the human p53 core domain in the absence of DNA.
Authors: Wang, Y. / Rosengarth, A. / Luecke, H.
History
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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: P53 TUMOR SUPPRESSOR
B: P53 TUMOR SUPPRESSOR
C: P53 TUMOR SUPPRESSOR
D: P53 TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6098
Polymers98,3484
Non-polymers2624
Water7,008389
1
A: P53 TUMOR SUPPRESSOR
hetero molecules


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


Theoretical massNumber of molelcules
Total (without water)24,6522
Polymers24,5871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: P53 TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6522
Polymers24,5871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: P53 TUMOR SUPPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6522
Polymers24,5871
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.913, 69.364, 84.179
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
P53 TUMOR SUPPRESSOR / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 24586.877 Da / Num. of mol.: 4 / Fragment: core domain (residues 94-312)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSE420 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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.: 389 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 2 ul protein solution (5 mg/ml protein in 20 mM Tris, pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 ul reservoir buffer consisting of 100 mM Hepes, pH 7.6, 10 mM DTT, and 14-21% (w/v) ...Details: 2 ul protein solution (5 mg/ml protein in 20 mM Tris, pH 7.6, 150 mM NaCl, 10 mM DTT) were mixed with 2 ul reservoir buffer consisting of 100 mM Hepes, pH 7.6, 10 mM DTT, and 14-21% (w/v) polyethylene glycol (PEG) 4000 above 500 ul reservoir buffer. Colorless plate-shaped crystals were obtained within a few days. VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.5418
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 24, 2004
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 49562 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.162 / Χ2: 0.794 / Net I/σ(I): 26.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 6.7 / Num. unique all: 4839 / Χ2: 0.694 / % possible all: 98.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å42.11 Å
Translation3 Å42.11 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1TSR, chain B

1tsr


Resolution: 2.05→50 Å / σ(I): 2
RfactorNum. reflection% reflection
Rfree0.246 4614 9.2 %
Rwork0.209 --
all-49982 -
obs-49521 99.1 %
Solvent computationBsol: 36.247 Å2
Displacement parametersBiso mean: 29.411 Å2
Baniso -1Baniso -2Baniso -3
1-10.411 Å20 Å20.293 Å2
2---16.469 Å20 Å2
3---6.058 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6096 0 4 389 6489
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.268
X-RAY DIFFRACTIONc_mcbond_it1.5141.5
X-RAY DIFFRACTIONc_scbond_it2.2212
X-RAY DIFFRACTIONc_mcangle_it2.4832
X-RAY DIFFRACTIONc_scangle_it3.3122.5
LS refinement shellResolution: 2.05→2.06 Å
RfactorNum. reflection% reflection
Rfree0.297 79 -
Rwork0.239 --
obs-851 1.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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