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

基本情報

• 登録情報: データベース: PDB / ID: 1olh
• タイトル: HIGH-RESOLUTION SOLUTION STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF P53 BY MULTI-DIMENSIONAL NMR
• 要素: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN)
• キーワード: ANTI-ONCOGENE PROTEIN

機能・相同性

分子機能:

negative regulation of helicase 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 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / regulation of cell cycle G2/M phase transition / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / germ cell nucleus / regulation of fibroblast apoptotic process / bone marrow development / cellular response to actinomycin D / circadian behavior / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / positive regulation of programmed necrotic cell death / T cell proliferation involved in immune response / : / 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 / regulation of DNA damage response, signal transduction by p53 class mediator / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / thymocyte apoptotic process / ER overload response / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / B cell lineage commitment / entrainment of circadian clock by photoperiod / negative regulation of DNA replication / negative regulation of mitophagy / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / necroptotic process / negative regulation of telomere maintenance via telomerase / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of release of cytochrome c from mitochondria / 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 / negative regulation of reactive oxygen species metabolic process / rRNA transcription / Transcriptional Regulation by VENTX / TFIID-class transcription factor complex binding / cellular response to UV-C / viral process / neuroblast proliferation / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / general transcription initiation factor binding / chromosome organization / hematopoietic stem cell differentiation / positive regulation of execution phase of apoptosis / embryonic organ development / type II interferon-mediated signaling pathway / response to X-ray / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / hematopoietic progenitor cell differentiation / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / glial cell proliferation / cellular response to glucose starvation / mitophagy / negative regulation of fibroblast proliferation / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / negative regulation of proteolysis / positive regulation of intrinsic apoptotic signaling pathway / response to salt stress / mitotic G1 DNA damage checkpoint signaling / cardiac muscle cell apoptotic process / transcription repressor complex / gastrulation / 14-3-3 protein binding / MDM2/MDM4 family protein binding / positive regulation of cardiac muscle cell apoptotic process / transforming growth factor beta receptor signaling pathway

ドメイン・相同性:

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

構成要素:

Cellular tumor antigen p53

• 生物種: Homo sapiens (ヒト)
• 手法: 溶液NMR
• データ登録者: Clore, G.M. / Omichinski, J.G. / Gronenborn, A.M.
• 引用: 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	1994年6月13日	処理サイト: BNL
改定 1.0	1995年3月31日	Provider: repository / タイプ: Initial release
改定 1.1	2008年3月24日	Group: Version format compliance
改定 1.2	2011年7月13日	Group: Version format compliance
改定 1.3	2022年2月23日	Group: Database references / Derived calculations / Other カテゴリ: 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
改定 1.4	2024年5月22日	Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

集合体

登録構造単位

A: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN)

B: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN)

C: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN)

D: TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN)

概要:

• 19.8 kDa, 4 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	19,795	4
ポリマ－	19,795	4
非ポリマー	0	0
水	0	0

1

概要:

• 登録構造と同一
• 登録者が定義した集合体

対称操作:

タイプ	名称	対称操作	数
identity operation	1_555	x,y,z	1

NMR アンサンブル

	データ	基準
コンフォーマー数 (登録 / 計算)	35 / -
代表モデル

要素

#1: タンパク質・ペプチド

A B C D
TUMOR SUPPRESSOR P53 (OLIGOMERIZATION DOMAIN)

詳細:

分子量: 4948.632 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 参照: UniProt: P04637

実験情報

実験

• 実験: 手法: 溶液NMR

解析

• 精密化: ソフトェア番号: 1 ; 詳細: 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アンサンブル: 登録したコンフォーマーの数: 35