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- PDB-1sae: HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION DOM... -

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Entry
Database: PDB / ID: 1sae
TitleHIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR (SAC STRUCTURES)
ComponentsTUMOR SUPPRESSOR P53
KeywordsANTI-ONCOGENE
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 / 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 / transcription coactivator binding / positive regulation of reactive oxygen species metabolic process / intracellular protein localization / histone deacetylase binding
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, 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.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: Refined solution structure of the oligomerization domain of the tumour suppressor p53.
Authors: Clore, G.M. / Ernst, J. / Clubb, R. / Omichinski, J.G. / Kennedy, W.M. / Sakaguchi, K. / Appella, E. / Gronenborn, A.M.
#1: Journal: Science / Year: 1995
Title: Interhelical Angles in the Solution Structure of the Oligomerization Domain of P53: Correction
Authors: Clore, G.M. / Omichinski, J.G. / Sakaguchi, K. / Zambrano, N. / Sakamoto, H. / Appella, E. / Gronenborn, A.M.
#2: Journal: 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
DepositionMar 12, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
SupersessionSep 30, 2008ID: 1SAG, 1SAI
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
B: TUMOR SUPPRESSOR P53
C: TUMOR SUPPRESSOR P53
D: TUMOR SUPPRESSOR P53


Theoretical massNumber of molelcules
Total (without water)19,7954
Polymers19,7954
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)77 / -
Representative

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Components

#1: Protein/peptide
TUMOR SUPPRESSOR P53


Mass: 4948.632 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: SAC STRUCTURES 1 - 26 / Source: (natural) Homo sapiens (human) / References: UniProt: P04637
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: 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 4472 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 4472 EXPERIMENTAL RESTRAINTS COMPRISING THE FOLLOWING INTRA- AND INTER-SUBUNIT RESTRAINTS: (A) INTRASUBUNIT: 852 SEQUENTIAL (|I-J|=1), 712 MEDIUM RANGE (1 < |I-J| >=5) AND 76 LONG RANGE (|I-J| >5) INTERRESIDUES AND 740 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS, 136 DISTANCE RESTRAINTS FOR 68 HYDROGEN BONDS, 284 TORSION ANGLE (144 PHI, 104 CHI1, AND 36 CHI2) RESTRAINTS, AND 144 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS. (B) INTERSUBUNIT: 244 A-B/C-D, 876 A-C/B-D, 40 A-D/B-C APPROXIMATE INTERPROTON DISTANCE RESTRAINTS, 40 DISTANCE RESTRAINTS FOR 20 HYDROGEN BONDS INVOLVING THE A-C/B-D SUBUNITS, AND 36 DISTANCE RESTRAINTS FOR 4 WATER MOLECULES. IN ADDITION, THERE ARE A TOTAL OF 38 CALPHA AND 35 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 B 106, 92-96 (1995)]. THE 77 STRUCTURES PRESENTED IN PDB ENTRIES 1SAE, 1SAG, AND 1SAI ARE CALCULATED WITH THE FOLLOWING VALUES FOR THE HARD SPHERE EFFECTIVE VAN DER WAALS RADII USED IN QUARTIC VAN DER WAALS REPULSION TERM. IN THE SOURCE REFERENCE, THESE STRUCTURES ARE REFERRED TO AS . H(POLAR) = 0.64 ANGSTROMS, H (NON-POLAR) = 1.17 ANGSTROMS, N = 1.24 ANGSTROMS, C = 1.44 ANGSTROMS, O = 1.19 ANGSTROMS, AND S = 1.52 ANGSTROMS. THESE VALUES CORRESPOND TO 0.8 TIMES THE VAN DER WAALS RADII EMPLOYED IN THE PARAM19/PARAM20 ENERGY PARAMETERS OF CHARMM. THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & GRONENBORN, A.M. (1988) FEBS LETT. 229, 317-324. ALL STRUCTURAL STATISTICS ARE GIVEN IN THE SOURCE REFERENCE. ENTRY 1SAK CONTAINS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE: (SA)R. THIS IS OBTAINED BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 77 DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO RESIDUES 326 - 354 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 COLUMN 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 COMPLETELY DISORDERED.
NMR ensembleConformers submitted total number: 77

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