- PDB-8jv0: Crystal structure of the SLA-2*1001 allele and ASFV antigenic pep... -
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基本情報
登録情報
データベース: PDB / ID: 8jv0
タイトル
Crystal structure of the SLA-2*1001 allele and ASFV antigenic peptide at 2.2A resolution
要素
Beta-2-microglobulinΒ2-ミクログロブリン
MHC class I antigen
TYR-MET-ASN-CYS-SER-LEU-PRO-THR-TYR
キーワード
IMMUNE SYSTEM (免疫系) / SLA / MHC I / IMMUNOLOGY ANTIGEN
機能・相同性
機能・相同性情報
ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / 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 ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / 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 / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / 免疫応答 / lysosomal membrane / external side of plasma membrane / signaling receptor binding / extracellular space / extracellular region 類似検索 - 分子機能
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Β2-ミクログロブリン / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Β2-ミクログロブリン / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold 類似検索 - ドメイン・相同性
A: MHC class I antigen B: Beta-2-microglobulin C: TYR-MET-ASN-CYS-SER-LEU-PRO-THR-TYR D: MHC class I antigen E: Beta-2-microglobulin F: TYR-MET-ASN-CYS-SER-LEU-PRO-THR-TYR
モノクロメーター: Si111 / 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: 0.987 Å / 相対比: 1
反射
解像度: 1.94→50 Å / Num. obs: 39759 / % possible obs: 98.4 % / 冗長度: 9.5 % / Rpim(I) all: 0.0267 / Net I/av σ(I): 0.25 / Net I/σ(I): 6
反射 シェル
解像度: 1.94→1.97 Å / Mean I/σ(I) obs: 0.25 / Num. unique obs: 3586 / Rsym value: 0.562
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.8.0258
精密化
HKL-3000
7.21
データ削減
HKL-3000
7.21
データスケーリング
PHASER
2.7.0
位相決定
精密化
構造決定の手法: 分子置換 / 解像度: 2.2→49.03 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.797 / SU ML: 0.187 / 交差検証法: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.264 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.24882
1859
5 %
RANDOM
Rwork
0.22182
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obs
0.22319
35066
72.34 %
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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: 1.2 Å / 溶媒モデル: MASK