+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1eez | ||||||
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タイトル | Crystal Structure Determination of HLA-A2.1 Complexed to GP2 Peptide Variant(I2L/V5L) | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / major histocompatibility complex (主要組織適合遺伝子複合体) / peptide binding (ペプチド) | ||||||
機能・相同性 | 機能・相同性情報 : / : / retina homeostasis / regulation of membrane depolarization / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna ...: / : / retina homeostasis / regulation of membrane depolarization / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / 免疫応答 / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / 小胞体 / ゴルジ体 / signaling receptor binding / focal adhesion / 自然免疫系 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 解像度: 2.3 Å | ||||||
データ登録者 | Sharma, A.K. / Kuhns, J.J. / Collins, E.J. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 2001 タイトル: Class I major histocompatibility complex anchor substitutions alter the conformation of T cell receptor contacts. 著者: Sharma, A.K. / Kuhns, J.J. / Yan, S. / Friedline, R.H. / Long, B. / Tisch, R. / Collins, E.J. #1: ジャーナル: J.Biol.Chem. / 年: 1999 タイトル: Poor Binding of HER-2/neu Epitope (GP2) to HLA-A2.1 is Due to a Lack of Interactions with the Center of the Peptide 著者: Kuhns, J.J. / Batalia, M.A. / Yan, S. / Collins, E.J. | ||||||
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 | 1eez.cif.gz | 159.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1eez.ent.gz | 129.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1eez.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/ee/1eez ftp://data.pdbj.org/pub/pdb/validation_reports/ee/1eez | 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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2 |
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単位格子 |
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詳細 | HLA_A2.1 heavy chain noncovalently associated to a beta-2-microglobulin subunit (light chain). Heavy chain is made of three sununits alpha1, alpha2 and alpha3. Peptide binds to the groove formed by the alpha1 and alpha2 domains |
-要素
#1: タンパク質 | 分子量: 31854.203 Da / 分子数: 2 / 断片: RESIDUES 1-275 OF EXTRACELLULAR PORTION / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: PLM1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01892, UniProt: P04439*PLUS #2: タンパク質 | 分子量: 11879.356 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: PLM1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01884, UniProt: P61769*PLUS #3: タンパク質・ペプチド | 分子量: 898.142 Da / 分子数: 2 / Mutation: I2L,V5L / 由来タイプ: 合成 詳細: The peptide was synthesized at the peptide synthesis facility of University of North Carolina at Chapel Hill. #4: 水 | ChemComp-HOH / | 構成要素の詳細 | HLA_A2.1 heavy chain noncovalently associated to a beta-2-microglobulin subunit (light chain). ...HLA_A2.1 heavy chain noncovalently associated to a beta-2-microglobulin subunit (light chain). Heavy chain is made of three subunits alpha1, alpha2 and alpha3. Peptide binds to the groove formed by the alpha1 and alpha2 domains. | |
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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: 2 |
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-試料調製
結晶 | マシュー密度: 2.48 Å3/Da / 溶媒含有率: 50.4 % | ||||||||||||||||||
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: 18% PEG8000, 25 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||
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: 100 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RU200 / 波長: 1.5418 |
検出器 | タイプ: RIGAKU RAXIS IIC / 検出器: IMAGE PLATE / 日付: 1999年9月30日 |
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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2.3→50 Å / Num. all: 114345 / Num. obs: 33403 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 2 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 4.73 |
反射 シェル | 解像度: 2.3→2.44 Å / 冗長度: 2 % / Rmerge(I) obs: 0.293 / Num. unique all: 5095 / % possible all: 84.8 |
反射 | *PLUS 最低解像度: 50 Å / Num. measured all: 114345 |
反射 シェル | *PLUS % possible obs: 84.8 % / Mean I/σ(I) obs: 2.4 |
-解析
ソフトウェア |
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精密化 | 解像度: 2.3→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 974700.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber / 詳細: Maximum likelihood function
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 28.79 Å2 / ksol: 0.384 e/Å3 | |||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 21.3 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.3→50 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.3→2.44 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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精密化 | *PLUS 最高解像度: 2.3 Å / 最低解像度: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.29 | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS | |||||||||||||||||||||||||
拘束条件 | *PLUS
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