+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1a6a | ||||||
---|---|---|---|---|---|---|---|
タイトル | THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3 | ||||||
要素 |
| ||||||
キーワード | COMPLEX (TRANSMEMBRANE/GLYCOPROTEIN) / MHC GLYCOPROTEIN / COMPLEX (TRANSMEMBRANE-GLYCOPROTEIN) / COMPLEX (TRANSMEMBRANE-GLYCOPROTEIN) complex | ||||||
機能・相同性 | 機能・相同性情報 immunoglobulin production involved in immunoglobulin-mediated immune response / negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / : / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding ...immunoglobulin production involved in immunoglobulin-mediated immune response / negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / : / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / positive regulation of cytokine-mediated signaling pathway / regulation of interleukin-4 production / regulation of interleukin-10 production / T cell activation involved in immune response / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / negative thymic T cell selection / autolysosome membrane / positive regulation of type 2 immune response / T cell selection / regulation of T-helper cell differentiation / positive regulation of prostaglandin biosynthetic process / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / negative regulation of viral entry into host cell / MHC class II receptor activity / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell activation / humoral immune response mediated by circulating immunoglobulin / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of mature B cell apoptotic process / positive thymic T cell selection / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / 液胞 / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of kinase activity / inflammatory response to antigenic stimulus / positive regulation of neutrophil chemotaxis / cytokine receptor activity / positive regulation of macrophage cytokine production / 中間径フィラメント / prostaglandin biosynthetic process / positive regulation of T cell differentiation / regulation of macrophage activation / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cytokine binding / nitric-oxide synthase binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / response to type II interferon / positive regulation of insulin secretion involved in cellular response to glucose stimulus / plasma membrane => GO:0005886 / negative regulation of DNA damage response, signal transduction by p53 class mediator / chaperone cofactor-dependent protein refolding / 液性免疫 / macrophage differentiation / negative regulation of type II interferon production / immunoglobulin mediated immune response / Generation of second messenger molecules / 免疫シナプス / antigen processing and presentation / PD-1 signaling / epidermis development / type II interferon-mediated signaling pathway / protein folding chaperone / positive regulation of B cell proliferation / positive regulation of chemokine production / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / エンドソーム / lysosomal lumen / negative regulation of cell migration / trans-Golgi network membrane / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / protein tetramerization / clathrin-coated endocytic vesicle membrane / intracellular protein transport / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / 認識 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / positive regulation of interleukin-6 production / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.75 Å | ||||||
データ登録者 | Ghosh, P. / Amaya, M. / Mellins, E. / Wiley, D.C. | ||||||
引用 | ジャーナル: Nature / 年: 1995 タイトル: The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3. 著者: Ghosh, P. / Amaya, M. / Mellins, E. / Wiley, D.C. | ||||||
履歴 |
|
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
---|
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1a6a.cif.gz | 88.2 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb1a6a.ent.gz | 69.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1a6a.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/a6/1a6a ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a6a | HTTPS FTP |
---|
-関連構造データ
関連構造データ | 1dlhS S: 精密化の開始モデル |
---|---|
類似構造データ |
-リンク
-集合体
登録構造単位 |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
単位格子 |
|
-要素
#1: タンパク質 | 分子量: 20469.172 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / Cell: B-LYMPHOCYTE / 細胞株: 9.5.3 / 細胞内の位置: PLASMA MEMBRANE細胞膜 / 参照: UniProt: P01903 | ||
---|---|---|---|
#2: タンパク質 | 分子量: 21935.385 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / Cell: B-LYMPHOCYTE / 細胞株: 9.5.3 / 細胞内の位置: PLASMA MEMBRANE細胞膜 / 参照: UniProt: P01912, UniProt: P01911*PLUS | ||
#3: タンパク質・ペプチド | 分子量: 1676.118 Da / 分子数: 1 / Fragment: CLIP FRAGMENT 87 - 101 OF INVARIANT CHAIN / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / Cell: B-LYMPHOCYTE / 細胞株: 9.5.3 / 細胞内の位置: PLASMA MEMBRANE細胞膜 / 参照: UniProt: P04233 | ||
#4: 糖 | #5: 水 | ChemComp-HOH / | |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 2 |
---|
-試料調製
結晶 | マシュー密度: 2.7 Å3/Da / 溶媒含有率: 52 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
結晶化 | pH: 4.5 詳細: 12% PEG 4K, 100 MM MGCL2, 100 MM ACETATE BUFFER, PH 4.5 | ||||||||||||||||||||||||
結晶化 | *PLUS 手法: unknown詳細: conditions similar to: Gorga, J.C., (1991) Res. Immun., 142, 401. | ||||||||||||||||||||||||
溶液の組成 | *PLUS
|
-データ収集
回折 | 平均測定温度: 100 K |
---|---|
放射光源 | 由来: シンクロトロン / サイト: CHESS / ビームライン: F1 / 波長: 0.918 |
検出器 | タイプ: FUJI / 検出器: IMAGE PLATE / 日付: 1994年7月1日 / 詳細: MIRRORS |
放射 | モノクロメーター: SI(111) / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.918 Å / 相対比: 1 |
反射 | 解像度: 2.75→15 Å / Num. obs: 14428 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / 冗長度: 3.2 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.7 |
反射 シェル | 解像度: 2.75→3 Å / 冗長度: 3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.3 / % possible all: 97.2 |
反射 | *PLUS Num. obs: 13021 |
反射 シェル | *PLUS % possible obs: 97.2 % |
-解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 1DLH 解像度: 2.75→6 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 詳細: RESIDUES 5 - 180 OF THE ALPHA SUBUNIT AND RESIDUES 5 - 191 OF THE BETA SUBUNIT ARE CLEARLY VISIBLE IN 2FO-FC ELECTRON DENSITY MAPS. THREE SMALL BREAKS IN MAIN-CHAIN DENSITY OCCUR IN LOOP ...詳細: RESIDUES 5 - 180 OF THE ALPHA SUBUNIT AND RESIDUES 5 - 191 OF THE BETA SUBUNIT ARE CLEARLY VISIBLE IN 2FO-FC ELECTRON DENSITY MAPS. THREE SMALL BREAKS IN MAIN-CHAIN DENSITY OCCUR IN LOOP REGIONS OF THE BETA 2 DOMAIN (AT BETA 109, 172, AND 189).
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 47.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.75→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2.75→2.86 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.1 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | *PLUS Rfactor obs: 0.373 |