+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2uwe | ||||||
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タイトル | Large CDR3a loop alteration as a function of MHC mutation | ||||||
要素 |
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キーワード | IMMUNE SYSTEM / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / GLYCOPROTEIN / TRANSMEMBRANE / MHC I / MEMBRANE / RECEPTOR / CLASS I MHC / HYPOTHETICAL PROTEIN / IMMUNOGLOBULIN DOMAIN / IMMUNOGLOBULIN / IMMUNE RESPONSE / TCR-PMHC COMPLEX / T CELL SIGNALING / DISEASE MUTATION | ||||||
機能・相同性 | 機能・相同性情報 EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / tail-anchored membrane protein insertion into ER membrane / T cell mediated cytotoxicity directed against tumor cell target / T cell receptor complex / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna ...EMC complex / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / tail-anchored membrane protein insertion into ER membrane / T cell mediated cytotoxicity directed against tumor cell target / T cell receptor complex / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / carbohydrate binding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / innate immune response / focal adhesion / signaling receptor binding 類似検索 - 分子機能 | ||||||
生物種 | HOMO SAPIENS (ヒト) MUS MUSCULUS (ハツカネズミ) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å | ||||||
データ登録者 | Miller, P.J. / Pazy, Y. / Conti, B. / Riddle, D. / Biddison, W.E. / Appella, E. / Collins, E.J. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2007 タイトル: Single Mhc Mutation Eliminates Enthalpy Associated with T Cell Receptor Binding. 著者: Miller, P.J. / Pazy, Y. / Conti, B. / Riddle, D. / Appella, E. / Collins, E.J. | ||||||
履歴 |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-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 | 2uwe.cif.gz | 335.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2uwe.ent.gz | 272.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2uwe.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
文書・要旨 | 2uwe_validation.pdf.gz | 492.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2uwe_full_validation.pdf.gz | 509.8 KB | 表示 | |
XML形式データ | 2uwe_validation.xml.gz | 57.1 KB | 表示 | |
CIF形式データ | 2uwe_validation.cif.gz | 78.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/uw/2uwe ftp://data.pdbj.org/pub/pdb/validation_reports/uw/2uwe | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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2 |
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単位格子 |
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-要素
-タンパク質 , 4種, 8分子 AHBIELFM
#1: タンパク質 | 分子量: 31824.176 Da / 分子数: 2 / 断片: ECTO-DOMAIN, RESIDUES 25-299 / 変異: YES / 由来タイプ: 組換発現 詳細: MUTATION OF HLA-A2.1 AT POSITION 163, THREONINE TO ALANINE 由来: (組換発現) HOMO SAPIENS (ヒト) / Variant: T163A / プラスミド: PLM1 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): RIL / 参照: UniProt: P01892, UniProt: P04439*PLUS #2: タンパク質 | 分子量: 11879.356 Da / 分子数: 2 / 断片: RESIDUES 21-119 / 由来タイプ: 組換発現 詳細: HAS EXTRA METHIONINE DUE TO ESCHERICHIA COLI EXPRESSION 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PHN1 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): RIL / 参照: UniProt: P61769 #4: タンパク質 | 分子量: 21656.322 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) MUS MUSCULUS (ハツカネズミ) / 株: B6 / Cell: T CELL / 細胞株: AHIII T CELL CLONE / プラスミド: PLM1 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): RIL #5: タンパク質 | 分子量: 26890.883 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) MUS MUSCULUS (ハツカネズミ) / 株: B6 / Cell: T CELL / 細胞株: AHIII T CELL CLONE / プラスミド: PLM1 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / Variant (発現宿主): RIL / 参照: UniProt: P04213*PLUS |
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-タンパク質・ペプチド / 非ポリマー , 2種, 212分子 CJ
#3: タンパク質・ペプチド | 分子量: 1049.263 Da / 分子数: 2 / 断片: RESIDUES 4-12 / 由来タイプ: 合成 詳細: SELF-PEPTIDE RECOGNIZED BY AHIII T CELL WHEN PRESENTED BY HLA-A2.1. 由来: (合成) HOMO SAPIENS (ヒト) / 参照: UniProt: Q9NPA0 #6: 水 | ChemComp-HOH / | |
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-詳細
構成要素の詳細 | ENGINEERED配列の詳細 | MUTANT T163A ADDITIONAL | |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.55 Å3/Da / 溶媒含有率: 51 % / 解説: NONE |
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結晶化 | pH: 7.8 / 詳細: 14% PEG 8000, 1 M NACL, 25 MM HEPES, PH 7.8 |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: APS / ビームライン: 22-BM / 波長: 1 |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 2005年3月3日 / 詳細: MIRRORS |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 1 Å / 相対比: 1 |
反射 | 解像度: 2.4→30 Å / Num. obs: 76682 / % possible obs: 83.9 % / Observed criterion σ(I): 0 / 冗長度: 2.76 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.3 |
反射 シェル | 解像度: 2.37→2.49 Å / 冗長度: 2.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.64 / % possible all: 67.2 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 1LP9 解像度: 2.4→121 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.898 / SU B: 21.998 / SU ML: 0.25 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.846 / ESU R Free: 0.351 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 52-58 IN THE TCR CHAINS E AND L ARE COMPLETELY DISORDERED AND THUS HAVE AN OCCUPANCY OF 0.0
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 36.94 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.4→121 Å
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拘束条件 |
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