- PDB-2uv3: Structure of the signal-regulatory protein (SIRP) alpha domain th... -
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基本情報
登録情報
データベース: PDB / ID: 2uv3
タイトル
Structure of the signal-regulatory protein (SIRP) alpha domain that binds CD47.
要素
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
キーワード
RECEPTOR / CD47-BINDING DOMAIN OF SIRP-ALPHA / MEMBRANE / SH3- BINDING / GLYCOPROTEIN / TRANSMEMBRANE / PHOSPHORYLATION / HUMAN SIRP-ALPHA N TERMINAL V DOMAIN / IMMUNOGLOBULIN DOMAIN / SIGNAL-REGULATORY PROTEIN ALPHA
機能・相同性
機能・相同性情報
negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / regulation of interleukin-1 beta production / regulation of type II interferon production / GTPase regulator activity / cell-cell adhesion mediator activity ...negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / regulation of interleukin-1 beta production / regulation of type II interferon production / GTPase regulator activity / cell-cell adhesion mediator activity / protein antigen binding / negative regulation of nitric oxide biosynthetic process / negative regulation of interferon-beta production / negative regulation of JNK cascade / regulation of tumor necrosis factor production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / regulation of interleukin-6 production / Signal regulatory protein family interactions / negative regulation of interleukin-6 production / tertiary granule membrane / ficolin-1-rich granule membrane / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / cellular response to interleukin-1 / positive regulation of phagocytosis / protein tyrosine kinase binding / negative regulation of protein phosphorylation / Cell surface interactions at the vascular wall / negative regulation of ERK1 and ERK2 cascade / negative regulation of inflammatory response / cellular response to type II interferon / SH3 domain binding / cellular response to hydrogen peroxide / cell migration / positive regulation of T cell activation / regulation of gene expression / cellular response to lipopolysaccharide / protein phosphatase binding / cell adhesion / Neutrophil degranulation / cell surface / extracellular exosome / membrane / plasma membrane 類似検索 - 分子機能
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.
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
ID
波長 (Å)
相対比
1
0.8856
1
2
0.9783
1
3
0.9079
1
4
0.9792
1
反射
解像度: 1.8→50 Å / Num. obs: 441122 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / 冗長度: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.1
反射 シェル
解像度: 1.8→1.86 Å / 冗長度: 3.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.8 / % possible all: 98
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.2.0019
精密化
HKL-2000
データ削減
SCALEPACK
データスケーリング
PHASER
位相決定
精密化
構造決定の手法: 分子置換 開始モデル: STRUCTURE DETERMINED BY MAD IN SPACE GROUP P21212 解像度: 1.8→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.713 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.13 / 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
0.249
1497
5.1 %
RANDOM
Rwork
0.204
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obs
0.207
28037
99 %
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溶媒の処理
イオンプローブ半径: 1 Å / 減衰半径: 1 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK