+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 1i7t | ||||||
---|---|---|---|---|---|---|---|
タイトル | CRYSTAL STRUCTURE OF CLASS I MHC A2 IN COMPLEX WITH PEPTIDE P1049-5V | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / MHC fold | ||||||
機能・相同性 | ![]() : / : / regulation of membrane depolarization / retina homeostasis / T cell mediated cytotoxicity directed against tumor cell target / 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 ...: / : / regulation of membrane depolarization / retina homeostasis / T cell mediated cytotoxicity directed against tumor cell target / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / cellular response to lipopolysaccharide / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Busslep, J. / Zhao, R. / Loftus, D. / Appella, E. / Collins, E.J. | ||||||
![]() | ![]() タイトル: T cell activity correlates with oligomeric peptide-major histocompatibility complex binding on T cell surface 著者: Busslep, J. / Zhao, R. / Donnini, D. / Loftus, D. / Saad, M. / Appella, E. / Collins, E.J. | ||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 157.6 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 131.3 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 464.1 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 488.2 KB | 表示 | |
XML形式データ | ![]() | 29.9 KB | 表示 | |
CIF形式データ | ![]() | 40.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
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: 31854.203 Da / 分子数: 2 / 断片: EXTRACELLULAR DOMAIN, RESIDUES 25-299 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #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) ![]() ![]() ![]() #3: タンパク質・ペプチド | 分子量: 1001.220 Da / 分子数: 2 / 由来タイプ: 合成 / 詳細: The nine residue peptide was chemically synthesized |
---|
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.48 Å3/Da / 溶媒含有率: 50.42 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
結晶化 | *PLUS 詳細: used microseeding | |||||||||||||||||||||||||
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: ![]() |
検出器 | タイプ: RIGAKU RAXIS II / 検出器: IMAGE PLATE |
放射 | モノクロメーター: Ni filter / 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: 2.8→30 Å / Num. all: 20521 / Num. obs: 20521 / % possible obs: 97 % / Observed criterion σ(I): -3 / 冗長度: 3.9 % / Biso Wilson estimate: 60.2 Å2 / Rmerge(I) obs: 0.148 / Rsym value: 0.148 / Net I/σ(I): 7 |
反射 シェル | 解像度: 2.75→2.85 Å / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 9 / Rsym value: 0.379 / % possible all: 96.7 |
反射 | *PLUS 最低解像度: 50 Å / % possible obs: 96.3 % |
反射 シェル | *PLUS % possible obs: 96.7 % |
-
解析
ソフトウェア |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]()
| |||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 13.3 Å2 | |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.8→30 Å
| |||||||||||||||||||||||||
拘束条件 |
| |||||||||||||||||||||||||
ソフトウェア | *PLUS 名称: REFMAC / 分類: refinement | |||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 2.8 Å / 最低解像度: 30 Å / σ(F): 0 / Rfactor obs: 0.23 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 13.3 Å2 | |||||||||||||||||||||||||
拘束条件 | *PLUS タイプ: p_angle_d / Dev ideal: 1.34 |