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- PDB-3sak: HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION DOM... -

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Entry
Database: PDB / ID: 3sak
TitleHIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR (SAC STRUCTURES)
ComponentsPROTEIN (TUMOR SUPPRESSOR P53)
KeywordsAPOPTOSIS/CELL CYCLE/GENE REGULATION / ANTI-ONCOGENE / P53 DOMAIN / APOPTOSIS-CELL CYCLE-GENE REGULATION COMPLEX
Function / homology
Function and homology information


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 / Activation of NOXA and translocation to mitochondria / 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 / 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 / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / 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 / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / chromosome organization / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / MDM2/MDM4 family protein binding / glial cell proliferation / embryonic organ development / cellular response to glucose starvation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / cardiac muscle cell apoptotic process / response to salt stress / transcription initiation-coupled chromatin remodeling / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation
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 / simulated annealing
AuthorsClore, G.M.
Citation
Journal: J.Am.Chem.Soc. / Year: 1999
Title: Improving the Packing and Accuracy of NMR Structure with a Pseudopotential for the Radius of Gyration
Authors: Kuszewski, J. / Gronenborn, A.M. / Clore, G.M.
#1: 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. / Poindexter Kennedy, W.M. / Sakaguchi, K. / Appella, E. / Gronenborn, A.M.
#2: 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.
#3: 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
DepositionApr 30, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Jun 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.classification
Revision 1.4Dec 27, 2023Group: 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: PROTEIN (TUMOR SUPPRESSOR P53)
B: PROTEIN (TUMOR SUPPRESSOR P53)
C: PROTEIN (TUMOR SUPPRESSOR P53)
D: PROTEIN (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_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 23SIMULATED ANNEALING
RepresentativeModel #1restrained minimized mean structure

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Components

#1: Protein/peptide
PROTEIN (TUMOR SUPPRESSOR P53)


Mass: 4948.632 Da / Num. of mol.: 4 / Fragment: OLIGOMERIZATION DOMAIN, RESIDUES 319 - 360 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04637
#2: Water ChemComp-HOH / water / 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
NMR experimentType: 3D AND 4D TRIPLE AND DOUBLE RESONANCE HETERONUCLEAR EXPERIMENTS

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Sample preparation

Sample conditionsTemperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameDeveloperClassification
XPLOR/CNSBRUNGER, A., CLORE, G.M. ET AL.refinement
XPLOR/CNSBRUNGER, A., CLORE, G.M. ET AL.structure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: TERMS IN THE TARGET FUNCTION USED FOR SIMULATED ANNEALING NOE (SUM AVERAGING) AND TORSION ANGLE RESTRAINTS 3JHNALPHA COUPLING CONSTANT RESTRAINTS (GARRETT ET AL J. MAGN. RESON. B104, 99-103 ...Details: TERMS IN THE TARGET FUNCTION USED FOR SIMULATED ANNEALING NOE (SUM AVERAGING) AND TORSION ANGLE RESTRAINTS 3JHNALPHA COUPLING CONSTANT RESTRAINTS (GARRETT ET AL J. MAGN. RESON. B104, 99-103 (1994). TERM FOR THE RADIUS OF GYRATION (KUSZEWSKI J, GRONENB CLORE, GM J AM CHEM SOC 121, 2337-2338 (1999)) TORSION ANGLE DATABASE POTENTIAL (KUSZEWSKI J, GRONEN CLORE GM. PROTEIN SCI 5, 1067-1080 (1996); J. MAGN 125, 171-177 (1997). COVALENT GEOMETRY RESTRAINTS (BONDS, ANGLES, IMPROPER QUARTIC VAN DER WAALS REPULSION TERM (NILGES. M, GRONENBORN, A.M., BRUNGER, A.T., CLORE, G.M. (1988) PROTEIN ENG. 2, 27-38). 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 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. THIS ENTRY CONTAINS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE, FOLLOWED BY THE 22 INDIVIDUAL SIMULATED ANNEALING STRUCTURES. THE RESTRAINED MINIMIZED MEAN STRUCTURE IS OBTAI BY FIRST AVERAGING COORDINATES OF THE INDIVIDUAL 22 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 OF THE RESTRAINED MINIMIZED MEA STRUCTURE (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. TERMS IN THE TARGET FUNCTION USED FOR SIMULATED ANNEALING: NOE (SUM AVERAGING) AND TORSION ANGLE RESTRAINTS 3JHNALPHA COUPLING CONSTANT RESTRAINTS (GARRETT ET AL J. MAGN. RESON. B104, 99-103 (1994). TERM FOR THE RADIUS OF GYRATION (KUSZEWSKI J, GRONENB CLORE, GM J AM CHEM SOC 121, 2337-2338 (1999)) TORSION ANGLE DATABASE POTENTIAL (KUSZEWSKI J, GRONEN CLORE GM. PROTEIN SCI 5, 1067-1080 (1996); J. MAGN 125, 171-177 (1997). COVALENT GEOMETRY RESTRAINTS (BONDS, ANGLES, IMPROPER QUARTIC VAN DER WAALS REPULSION TERM (NILGES. M, GRONENBORN, A.M., BRUNGER, A.T., CLORE, G.M. (1988) PROTEIN ENG. 2, 27-38). 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 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. THIS ENTRY CONTAINS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE, FOLLOWED BY THE 22 INDIVIDUAL SIMULATED ANNEALING STRUCTURES. THE RESTRAINED MINIMIZED MEAN STRUCTURE IS OBTAI BY FIRST AVERAGING COORDINATES OF THE INDIVIDUAL 22 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 OF THE RESTRAINED MINIMIZED MEA STRUCTURE (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 representativeSelection criteria: restrained minimized mean structure
NMR ensembleConformer selection criteria: SIMULATED ANNEALING / Conformers calculated total number: 23 / Conformers submitted total number: 23

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