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- PDB-1olh: HIGH-RESOLUTION SOLUTION STRUCTURE OF THE OLIGOMERIZATION DOMAIN ... -

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Entry
Database: PDB / ID: 1olh
TitleHIGH-RESOLUTION SOLUTION STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR
ComponentsTUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN)
KeywordsANTI-ONCOGENE PROTEIN
Function / homology
Function and homology information


Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / 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 ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / 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 / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / 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 / 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 / T cell lineage commitment / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / B cell lineage commitment / thymocyte apoptotic process / 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 / rRNA transcription / 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 / T cell proliferation involved in immune response / negative regulation of reactive oxygen species metabolic process / positive regulation of execution phase of apoptosis / Transcriptional Regulation by VENTX / replicative senescence / cellular response to UV-C / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to actinomycin D / neuroblast proliferation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / hematopoietic stem cell differentiation / type II interferon-mediated signaling pathway / Pyroptosis / viral process / chromosome organization / embryonic organ development / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / glial cell proliferation / hematopoietic progenitor cell differentiation / core promoter sequence-specific DNA binding / 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 cardiac muscle cell apoptotic process / positive regulation of intrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / negative regulation of proteolysis / Regulation of TP53 Activity through Acetylation / mitotic G1 DNA damage checkpoint signaling / gastrulation / 14-3-3 protein binding / response to salt stress / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription repressor complex
Similarity search - Function
p53, subunit A / p53-like tetramerisation domain / 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, subunit A / p53-like tetramerisation domain / 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 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsClore, G.M. / Omichinski, J.G. / Gronenborn, A.M.
CitationJournal: Science / Year: 1994
Title: High-resolution structure of the oligomerization domain of p53 by multidimensional NMR.
Authors: Clore, G.M. / Omichinski, J.G. / Sakaguchi, K. / Zambrano, N. / Sakamoto, H. / Appella, E. / Gronenborn, A.M.
History
DepositionJun 13, 1994Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN)
B: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN)
C: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN)
D: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN)


Theoretical massNumber of molelcules
Total (without water)19,7954
Polymers19,7954
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / -
Representative

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Components

#1: Protein/peptide
TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN)


Mass: 4948.632 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P04637

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Processing

RefinementSoftware ordinal: 1
Details: THE 3D STRUCTURE OF THE OLIGOMERIZATION DOMAIN (RESIDUES 319 - 360) OF P53 BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 3824 EXPERIMENTAL RESTRAINTS COMPRISING THE ...Details: THE 3D STRUCTURE OF THE OLIGOMERIZATION DOMAIN (RESIDUES 319 - 360) OF P53 BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 3824 EXPERIMENTAL RESTRAINTS COMPRISING THE FOLLOWING INTRA- AND INTER-SUBUNIT RESTRAINTS: (A) INTRASUBUNIT: 840 SEQUENTIAL (|I-J|=1), 744 SHORT RANGE (1 < |I-J| >=5) AND 72 LONG RANGE (|I-J| >5) INTERRESIDUES AND INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS, 136 DISTANCE RESTRAINTS FOR 68 HYDROGEN BONDS, 268 TORSION ANGLE (144 PHI, 104 CHI1 AND 20 CHI2) RESTRAINTS, AND 144 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS. (B) INTERSUBUNIT: 96 A-B/C-D, 758 A-C/B-D, 10 A-D/B-C APPROXIMATE INTERPROTON DISTANCE RESTRAINTS, AND 24 DISTANCE RESTRAINTS FOR 12 HYDROGEN BONDS INVOLVING THE A-C/B-D SUBUNITS. IN ADDITION, THERE ARE A TOTAL OF 38 CALPHA AND 38 CB CHEMICAL SHIFT RESTRAINTS PER SUBUNIT THAT HAVE BEEN INCORPORATED INTO THE REFINEMENT [J. KUSZWESKI, J. QIN, A.M. GRONENBORN AND G.M. CLORE, J. MAGN RESON. SER IN PRESS (1994)] THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. AND GRONENBORN, A.M. (1988) FEBS LETT. 29, 317-324. ALL STRUCTURAL STATISTICS ARE GIVEN IN THE JRNL REFERENCE. THE RESTRAINED MINIMIZED AVERAGE STRUCTURE (SA)R IS PRESENTED IN PROTEIN DATA BANK ENTRY 1OLG. THIS IS OBTAINED BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 35 DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO RESIDUES 324 - 356 OF ALL FOUR SUBUNITS, AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE QUANTITY PRESENTED IN COLUMNS 61 - 66 IN THIS SET OF COORDINATES (THE B-FACTOR FIELD IN X-RAY STRUCTURES) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE. THE NUMBERS IN COLUMNS 61 - 66 OF THE INDIVIDUAL STRUCTURES HAVE NO MEANING. NOTE THAT RESIDUES 319 - 323 AT THE N-TERMINUS AND RESIDUES 357 - 360 AT THE C-TERMINUS ARE DISORDERED.
NMR ensembleConformers submitted total number: 35

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