PDB-2g57: Structure of the Phosphorylation Motif of the oncogenic Protein b...

基本情報

• 登録情報: データベース: PDB / ID: 2g57
• タイトル: Structure of the Phosphorylation Motif of the oncogenic Protein beta-Catenin Recognized By a Selective Monoclonal Antibody
• 要素: Beta-catenin
• キーワード: ONCOPROTEIN / beta-Catenin oncogenic Protein / P-beta-Catenin phosphorylated peptide / epitope mapping / Antibody / P-beta-Catenin-Antibody complex / STD-NMR / TRNOESY / restrained molecular dynamics / bound structure / binding fragment

機能・相同性

分子機能:

positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / beta-catenin-ICAT complex / CDH11 homotypic and heterotypic interactions / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / neural plate development / metanephros morphogenesis / glial cell fate determination / Regulation of CDH19 Expression and Function / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / negative regulation of mitotic cell cycle, embryonic / Binding of TCF/LEF:CTNNB1 to target gene promoters / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / central nervous system vasculogenesis / regulation of centriole-centriole cohesion / RUNX3 regulates WNT signaling / regulation of centromeric sister chromatid cohesion / Regulation of CDH11 function / embryonic axis specification / Specification of the neural plate border / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / regulation of fibroblast proliferation / beta-catenin-TCF complex / endodermal cell fate commitment / acinar cell differentiation / dorsal root ganglion development / synaptic vesicle clustering / proximal/distal pattern formation / neuron fate determination / Formation of the nephric duct / endothelial tube morphogenesis / positive regulation of fibroblast growth factor receptor signaling pathway / dorsal/ventral axis specification / sympathetic ganglion development / fungiform papilla formation / layer formation in cerebral cortex / positive regulation of endothelial cell differentiation / presynaptic active zone cytoplasmic component / mesenchymal to epithelial transition / hindbrain development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / fascia adherens / regulation of protein localization to cell surface / ectoderm development / embryonic foregut morphogenesis / hair cell differentiation / detection of muscle stretch / cellular response to indole-3-methanol / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / mesenchymal cell proliferation involved in lung development / positive regulation of myoblast proliferation / histone methyltransferase binding / alpha-catenin binding / regulation of calcium ion import / regulation of epithelial to mesenchymal transition / Germ layer formation at gastrulation / positive regulation of homotypic cell-cell adhesion / negative regulation of oligodendrocyte differentiation / establishment of blood-retinal barrier / flotillin complex / apicolateral plasma membrane / epithelial cell differentiation involved in prostate gland development / cranial skeletal system development / positive regulation of epithelial cell proliferation involved in prostate gland development / cell-cell adhesion mediated by cadherin / male genitalia development / Formation of definitive endoderm / epithelial cell proliferation involved in prostate gland development / regulation of smooth muscle cell proliferation / catenin complex / beta-catenin destruction complex / embryonic brain development / oocyte development / lung-associated mesenchyme development / midbrain dopaminergic neuron differentiation / establishment of blood-brain barrier / Formation of axial mesoderm / negative regulation of protein sumoylation / Apoptotic cleavage of cell adhesion proteins / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated

ドメイン・相同性:

Beta-catenin / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold

構成要素:

Catenin beta-1 / Beta-catenin

• 手法: 溶液NMR / distance geometry, simulated annealing, torsion angle dynamics
• データ登録者: Megy, S. / Bertho, G. / Gharbi-Benarous, J. / Baleux, F. / Benarous, R. / Girault, J.P.
• 引用: ジャーナル: Febs Lett. / 年: 2006; タイトル: STD and TRNOESY NMR studies for the epitope mapping of the phosphorylation motif of the oncogenic protein beta-catenin recognized by a selective monoclonal antibody; 著者: Megy, S. / Bertho, G. / Gharbi-Benarous, J. / Baleux, F. / Benarous, R. / Girault, J.P.

履歴

登録	2006年2月22日	登録サイト: RCSB / 処理サイト: PDBJ
改定 1.0	2006年3月28日	Provider: repository / タイプ: Initial release
改定 1.1	2008年5月1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3月9日	Group: Data collection / Database references / Derived calculations カテゴリ: database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
改定 1.4	2024年11月13日	Group: Data collection / Structure summary カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

集合体

登録構造単位

A: Beta-catenin

概要:

• 2.93 kDa, 1 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)	2,929	1
ポリマ－	2,929	1
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)	10 / 20	structures with the least restraint violations
代表モデル	モデル #1	lowest energy

要素

#1: タンパク質・ペプチド

A Beta-catenin

詳細:

分子量: 2928.948 Da / 分子数: 1 / 断片: Residues 19-44 / 由来タイプ: 合成 / 詳細: This sequence occurs naturally in humans. / 参照: UniProt: P35222, UniProt: Q0PNE9*PLUS

• Has protein modification: Y

実験情報

実験

• 実験: 手法: 溶液NMR
• NMR実験: タイプ: 2D NOESY

試料調製

• 詳細: 内容: 1mM P-beta-Cat peptide with 0.01mM antibody; 20mM phosphate buffered saline(pH 7.4); 15mM sodium azide; 90% H2O, 10% D2O; 溶媒系: 90% H2O/10% D2O
• 試料状態: イオン強度: 20mM / pH: 7.4 / 圧: 1 atm / 温度: 278 K

NMR測定

• NMRスペクトロメーター: タイプ: Bruker AVANCE / 製造業者: Bruker / モデル: AVANCE / 磁場強度: 500 MHz

解析

NMR software

名称	バージョン	分類
XwinNMR		collection
Felix		データ解析
ARIA	1.2	精密化

• 精密化: 手法: distance geometry, simulated annealing, torsion angle dynamics; ソフトェア番号: 1
• 代表構造: 選択基準: lowest energy
• NMRアンサンブル: コンフォーマー選択の基準: structures with the least restraint violations; 計算したコンフォーマーの数: 20 / 登録したコンフォーマーの数: 10