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基本情報

登録情報
データベース: PDB / ID: 3sak
タイトルHIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR (SAC STRUCTURES)
要素PROTEIN (TUMOR SUPPRESSOR P53)
キーワードAPOPTOSIS/CELL CYCLE/GENE REGULATION / ANTI-ONCOGENE / P53 DOMAIN / APOPTOSIS-CELL CYCLE-GENE REGULATION COMPLEX
機能・相同性
機能・相同性情報


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 / type II interferon-mediated signaling pathway / hematopoietic stem cell differentiation / Pyroptosis / chromosome organization / viral process / 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
類似検索 - 分子機能
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
類似検索 - ドメイン・相同性
Cellular tumor antigen p53
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法溶液NMR / simulated annealing
データ登録者Clore, G.M.
引用
ジャーナル: J.Am.Chem.Soc. / 年: 1999
タイトル: Improving the Packing and Accuracy of NMR Structure with a Pseudopotential for the Radius of Gyration
著者: Kuszewski, J. / Gronenborn, A.M. / Clore, G.M.
#1: ジャーナル: Nat.Struct.Biol. / 年: 1995
タイトル: Refined Solution Structure of the Oligomerization Domain of the Tumour Suppressor P53
著者: Clore, G.M. / Ernst, J. / Clubb, R. / Omichinski, J.G. / Poindexter Kennedy, W.M. / Sakaguchi, K. / Appella, E. / Gronenborn, A.M.
#2: ジャーナル: Science / 年: 1995
タイトル: Interhelical Angles in the Solution Structure of the Oligomerization Domain of P53: Correction
著者: Clore, G.M. / Omichinski, J.G. / Sakaguchi, K. / Zambrano, N. / Sakamoto, H. / Appella, E. / Gronenborn, A.M.
#3: ジャーナル: Science / 年: 1994
タイトル: High-Resolution Structure of the Oligomerization Domain of P53 by Multidimensional NMR
著者: Clore, G.M. / Omichinski, J.G. / Sakaguchi, K. / Zambrano, N. / Sakamoto, H. / Appella, E. / Gronenborn, A.M.
履歴
登録1999年4月30日登録サイト: RCSB / 処理サイト: NDB
改定 1.01999年6月25日Provider: repository / タイプ: Initial release
改定 1.12008年4月26日Group: Version format compliance
改定 1.22011年7月13日Group: Version format compliance
改定 1.32021年11月3日Group: Data collection / Database references / Derived calculations
カテゴリ: 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
改定 1.42023年12月27日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: PROTEIN (TUMOR SUPPRESSOR P53)
B: PROTEIN (TUMOR SUPPRESSOR P53)
C: PROTEIN (TUMOR SUPPRESSOR P53)
D: PROTEIN (TUMOR SUPPRESSOR P53)


分子量 (理論値)分子数
合計 (水以外)19,7954
ポリマ－19,7954
非ポリマー00
水724
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_5551
NMR アンサンブル
データ基準
コンフォーマー数 (登録 / 計算)23 / 23SIMULATED ANNEALING
代表モデルモデル #1restrained minimized mean structure

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要素

#1: タンパク質・ペプチド
PROTEIN (TUMOR SUPPRESSOR P53)


分子量: 4948.632 Da / 分子数: 4 / 断片: OLIGOMERIZATION DOMAIN, RESIDUES 319 - 360 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P04637
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 4 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: 溶液NMR
NMR実験タイプ: 3D AND 4D TRIPLE AND DOUBLE RESONANCE HETERONUCLEAR EXPERIMENTS

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試料調製

試料状態温度: 308 K
結晶化
*PLUS
手法: other / 詳細: NMR

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NMR測定

NMRスペクトロメーター
タイプ製造業者モデル磁場強度 (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DMXBrukerDMX6002

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解析

NMR software
名称開発者分類
XPLOR/CNSBRUNGER, A., CLORE, G.M. ET AL.精密化
XPLOR/CNSBRUNGER, A., CLORE, G.M. ET AL.structure calculation
精密化手法: simulated annealing / ソフトェア番号: 1
詳細: 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 ...詳細: 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.
代表構造選択基準: restrained minimized mean structure
NMRアンサンブルコンフォーマー選択の基準: SIMULATED ANNEALING / 計算したコンフォーマーの数: 23 / 登録したコンフォーマーの数: 23

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