+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1a3k | |||||||||
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タイトル | X-RAY CRYSTAL STRUCTURE OF THE HUMAN GALECTIN-3 CARBOHYDRATE RECOGNITION DOMAIN (CRD) AT 2.1 ANGSTROM RESOLUTION | |||||||||
要素 | GALECTIN-3ガレクチン3 | |||||||||
キーワード | GALECTIN / GALAPTIN / LECTIN (レクチン) / IGE-BINDING PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / protein phosphatase inhibitor activity / negative regulation of T cell receptor signaling pathway / positive chemotaxis / macrophage chemotaxis / regulation of T cell proliferation / positive regulation of calcium ion import / chemoattractant activity / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / 免疫シナプス / laminin binding / molecular condensate scaffold activity / epithelial cell differentiation / 好中球 / RNA splicing / secretory granule membrane / positive regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway / spliceosomal complex / positive regulation of protein localization to plasma membrane / 転写後修飾 / carbohydrate binding / collagen-containing extracellular matrix / protein phosphatase binding / ミトコンドリア内膜 / 自然免疫系 / Neutrophil degranulation / 細胞膜 / extracellular space / RNA binding / extracellular exosome / extracellular region / 核質 / 生体膜 / 細胞核 / 細胞膜 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / MULTIPLE ISOMORPHOUS METHOD / 解像度: 2.1 Å | |||||||||
データ登録者 | Seetharaman, J. / Kanigsberg, A. / Slaaby, R. / Leffler, H. / Barondes, S.H. / Rini, J.M. | |||||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 1998 タイトル: X-ray crystal structure of the human galectin-3 carbohydrate recognition domain at 2.1-A resolution. 著者: Seetharaman, J. / Kanigsberg, A. / Slaaby, R. / Leffler, H. / Barondes, S.H. / Rini, J.M. #1: ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 1994 タイトル: Structure of S-Lectin, a Developmentally Regulated Vertebrate Beta-Galactoside-Binding Protein 著者: Liao, D.I. / Kapadia, G. / Ahmed, H. / Vasta, G.R. / Herzberg, O. #2: ジャーナル: J.Biol.Chem. / 年: 1993 タイトル: X-Ray Crystal Structure of the Human Dimeric S-Lac Lectin, L-14-II, in Complex with Lactose at 2.9-A Resolution 著者: Lobsanov, Y.D. / Gitt, M.A. / Leffler, H. / Barondes, S.H. / Rini, J.M. | |||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1a3k.cif.gz | 45.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1a3k.ent.gz | 29.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1a3k.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a3k ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a3k | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 15603.933 Da / 分子数: 1 / 断片: CARBOHYDRATE RECOGNITION DOMAIN (CRD) / 由来タイプ: 組換発現 詳細: THE CRD WAS PRODUCED BY TYPE VII COLLAGENASE (SIGMA) DIGESTION OF THE N-TERMINAL DOMAIN 由来: (組換発現) Homo sapiens (ヒト) 解説: THE CRD WAS PRODUCED BY TYPE VII COLLAGENASE (SIGMA) DIGESTION OF THE N-TERMINAL DOMAIN 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P17931 |
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#2: 多糖 | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#3: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: X線回折 |
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-試料調製
結晶 | マシュー密度: 2.25 Å3/Da / 溶媒含有率: 48 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5 詳細: PROTEIN CRYSTALLIZED BY HANGING-DROP VAPOUR DIFFUSION METHOD FROM DROPS CONTAINING EQUAL VOLUMES OF PROTEIN(10-15MG/ML) IN CRYSTALLIZATION BUFFER CONTAINING 1MM LACTOSE OR 30 MM N- ...詳細: PROTEIN CRYSTALLIZED BY HANGING-DROP VAPOUR DIFFUSION METHOD FROM DROPS CONTAINING EQUAL VOLUMES OF PROTEIN(10-15MG/ML) IN CRYSTALLIZATION BUFFER CONTAINING 1MM LACTOSE OR 30 MM N-ACETYLLACTOSAMINE AND THE WELL SOLUTION COMPOSED OF 27-30% PEG 4000-6000, 100MM TRIS-HCL PH 8.5, 100 MM MGCL2, AND 8 MM 2-MERCAPTOETHANOL., vapor diffusion - hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法, ハンギングドロップ法 | |||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 287 K |
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放射光源 | 由来: 回転陽極 / タイプ: その他 / 波長: 1.5418 |
検出器 | タイプ: SIEMENS / 検出器: AREA DETECTOR / 日付: 1994年12月1日 |
放射 | 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 1.9→25 Å / Num. obs: 7955 / % possible obs: 99 % / Rmerge(I) obs: 0.052 |
反射 | *PLUS Num. measured all: 40093 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: MULTIPLE ISOMORPHOUS METHOD / 解像度: 2.1→5 Å / σ(F): 2 詳細: THE STRUCTURE WAS SOLVED BY THE MULTIPLE ISOMORPHOUS REPLACEMENT METHOD. THE MODEL CONSISTS OF THE 137 AMINO ACID RESIDUE CARBOHYDRATE RECOGNITION DOMAIN IN COMPLEX WITH N-ACETYLLACTOSAMINE ...詳細: THE STRUCTURE WAS SOLVED BY THE MULTIPLE ISOMORPHOUS REPLACEMENT METHOD. THE MODEL CONSISTS OF THE 137 AMINO ACID RESIDUE CARBOHYDRATE RECOGNITION DOMAIN IN COMPLEX WITH N-ACETYLLACTOSAMINE AND 120 WATER MOLECULES. THIS STRUCTURE REPRESENTS A CRD DETERMINED FROM A GALECTIN WHICH DOES NOT SHOW THE CANONICAL 2-FOLD SYMMETRIC DIMER ORGANIZATION SHOWN BY GALECTINS-1 AND -2. COMPARISON WITH GALECTINS-1 AND -2 PROVIDES AN EXPLANATION FOR THE DIFFERENCES IN CARBOHYDRATE-BINDING SPECIFICITY SHOWN BY GALECTIN-3, AND FOR THE FACT THAT IT FAILS TO FORM DIMERS BY ANALOGOUS CRD-CRD INTERACTIONS.
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原子変位パラメータ | Biso mean: 20.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.1→5 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.1→3.13 Å / Total num. of bins used: 25 /
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Xplor file |
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