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

基本情報

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

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 / 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 / positive regulation of mitochondrial membrane permeability / mRNA transcription / positive regulation of programmed necrotic cell death / bone marrow development / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / TP53 Regulates Transcription of Death Receptors and Ligands / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / 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 / thymocyte apoptotic process / B cell lineage commitment / 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 / 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 / positive regulation of execution phase of apoptosis / replicative senescence / general transcription initiation factor binding / cellular response to UV-C / cellular response to actinomycin D / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / hematopoietic stem cell differentiation / Pyroptosis / viral process / embryonic organ development / chromosome organization / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / glial cell proliferation / hematopoietic progenitor cell differentiation / core promoter sequence-specific DNA binding / positive regulation of cardiac muscle cell apoptotic process / 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 intrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / Regulation of TP53 Activity through Acetylation / gastrulation / mitotic G1 DNA damage checkpoint signaling / response to salt stress / 14-3-3 protein binding / MDM2/MDM4 family protein binding / negative regulation of proteolysis / cardiac muscle cell apoptotic process / transcription repressor complex

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: 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. / Kennedy, W.M. / Sakaguchi, K. / Appella, E. / Gronenborn, A.M.

#1: 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.

#2: 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	1995年3月12日	処理サイト: BNL
改定 1.0	1995年10月15日	Provider: repository / タイプ: Initial release
改定 1.1	2008年3月24日	Group: Version format compliance
置き換え	2008年7月1日	ID: 1SAH
置き換え	2008年7月1日	ID: 1SAJ
改定 1.2	2011年7月13日	Group: Version format compliance
改定 1.3	2012年1月11日	Group: Other
改定 1.4	2024年5月1日	Group: Data collection / Database references / Other カテゴリ: chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

集合体

登録構造単位

A: TUMOR SUPPRESSOR P53

B: TUMOR SUPPRESSOR P53

C: TUMOR SUPPRESSOR P53

D: TUMOR SUPPRESSOR P53

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	72	4

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)	76 / -
代表モデル

要素

#1: タンパク質・ペプチド

A B C D
TUMOR SUPPRESSOR P53

詳細:

分子量: 4948.632 Da / 分子数: 4 / 由来タイプ: 天然 / 詳細: SAD STRUCTURES / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P04637

#2: 水

ChemComp-HOH / water

詳細:

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

実験情報

実験

• 実験: 手法: 溶液NMR

試料調製

• 結晶化: 手法: other / 詳細: 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 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 76 STRUCTURES PRESENTED IN PDB ENTRIES 1SAF, 1SAH, AND 1SAJ 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) = 0.95 ANGSTROMS, H (NON-POLAR) = 1.00 ANGSTROMS, N = 1.30 ANGSTROMS, C = 1.40 ANGSTROMS, C(AROMATIC) = 1.35 ANGSTROMS, O = 1.20 ANGSTROMS, AND S = 1.60 ANGSTROMS. THESE VALUES CORRESPOND TO THE HARD SPHERE EFFECTIVE VAN DER WAALS RADII EMPLOYED BY THE PROGRAMS DISMAN AND DIANA. 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 1SAL CONTAINS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE: (SA)R. THIS IS OBTAINED BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 76 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アンサンブル: 登録したコンフォーマーの数: 76