- PDB-3sdc: Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in comp... -
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基本情報
登録情報
データベース: PDB / ID: 3sdc
タイトル
Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-globotrihexosylceramide
要素
Antigen-presenting glycoprotein CD1d1
Beta-2-microglobulin
NKT TCR Valpha14 chain
NKT TCR autoreactive-Vbeta6 chain
キーワード
IMMUNE SYSTEM / CD1d / autoimmunity / self-recognition / NKT
機能・相同性
機能・相同性情報
regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / alpha-beta T cell receptor complex ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / alpha-beta T cell receptor complex / positive thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-4 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / antigen processing and presentation / Generation of second messenger molecules / regulation of immune response / PD-1 signaling / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / response to bacterium / 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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of type II interferon production / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / late endosome / Downstream TCR signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / endosome membrane / early endosome / lysosome / immune response / external side of plasma membrane / lysosomal membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol 類似検索 - 分子機能
: / T-cell receptor alpha chain, constant domain / MHC-I family domain / Domain of unknown function (DUF1968) / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / : / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...: / T-cell receptor alpha chain, constant domain / MHC-I family domain / Domain of unknown function (DUF1968) / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / : / Beta-2-Microglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta 類似検索 - ドメイン・相同性
1. SEQUENCE CONFLICT IN ENTITY 1 IS BASED ON REFERENCE 3 OF DATABASE P11609 (CD1D1_MOUSE). 2. THE ...1. SEQUENCE CONFLICT IN ENTITY 1 IS BASED ON REFERENCE 3 OF DATABASE P11609 (CD1D1_MOUSE). 2. THE SEQUENCE CONFLICT OF ENTITY 2 IS A NATURAL VARIANT ACCORDING TO DATABASE P01887 (B2MG_MOUSE).
モノクロメーター: graphite / プロトコル: SINGLE WAVELENGTH / 散乱光タイプ: x-ray
放射波長
相対比: 1
反射
解像度: 3.1→89.657 Å / Num. all: 23961 / Num. obs: 23961 / % possible obs: 98.4 % / 冗長度: 5.6 % / Rsym value: 0.222 / Net I/σ(I): 6.9
反射 シェル
Rmerge(I) obs: 0.01 / Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Rmerge(I) all
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rpim(I) all
Rrim(I) all
Rsym value
Net I/σ(I) obs
% possible all
3.1-3.27
6
1.124
0.8
20743
3451
0.447
1.124
1.028
1.7
99.1
3.27-3.47
5.9
0.712
1.2
19226
3263
0.285
0.712
0.65
2.7
99.1
3.47-3.71
5.8
0.479
1.8
17902
3090
0.194
0.479
0.436
4
98.9
3.71-4
5.7
0.326
2.6
16390
2865
0.133
0.326
0.297
5.5
98.7
4-4.38
5.6
0.21
4
14830
2650
0.086
0.21
0.19
8.2
98.7
4.38-4.9
5.4
0.148
5.6
13175
2421
0.061
0.148
0.134
10.4
98.3
4.9-5.66
5.3
0.153
5.4
11304
2123
0.064
0.153
0.138
9.9
97.6
5.66-6.93
5
0.156
5.2
9128
1824
0.067
0.156
0.14
9.1
97.8
6.93-9.8
5.4
0.094
7.8
7581
1413
0.039
0.094
0.085
14.4
95.5
9.8-66.716
5.9
0.084
6.7
5071
861
0.034
0.084
0.077
19.9
96.1
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解析
ソフトウェア
名称
バージョン
分類
NB
MOSFLM
データ削減
SCALA
3.3.15
データスケーリング
REFMAC
精密化
PDB_EXTRACT
3.1
データ抽出
精密化
構造決定の手法: 分子置換 / 解像度: 3.1→66.72 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.853 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7502 / SU B: 24.791 / SU ML: 0.425 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.504 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
Rfactor
反射数
%反射
Selection details
Rfree
0.2921
1225
5.1 %
RANDOM
Rwork
0.2402
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-
-
obs
0.2429
23951
97.52 %
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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