+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2jjs | |||||||||
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タイトル | Structure of human CD47 in complex with human signal regulatory protein (SIRP) alpha | |||||||||
要素 |
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キーワード | CELL ADHESION (細胞接着) / SIGNAL REGULATORY PROTEIN ALPHA / IMMUNOGLOBULIN SUPERFAMILY (免疫グロブリンスーパーファミリー) / TRANSMEMBRANE (膜貫通型タンパク質) / PHOSPHOPROTEIN / PAIRED RECEPTOR / POLYMORPHISM / GLYCOPROTEIN (糖タンパク質) / PYRROLIDONE CARBOXYLIC ACID (ピログルタミン酸) / ALTERNATIVE SPLICING (選択的スプライシング) / IMMUNOGLOBULIN DOMAIN (免疫グロブリンフォールド) / SIRP / CD47 (CD47) / SIRPA / MEMBRANE (生体膜) / SH3-BINDING | |||||||||
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 / regulation of Fc receptor mediated stimulatory signaling pathway / 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 / positive regulation of monocyte extravasation / regulation of interleukin-1 beta production / regulation of type II interferon production ...negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / regulation of Fc receptor mediated stimulatory signaling pathway / 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 / positive regulation of monocyte extravasation / regulation of interleukin-1 beta production / regulation of type II interferon production / ATP export / cell-cell adhesion mediator activity / GTPase regulator activity / positive regulation of cell-cell adhesion / regulation of interleukin-10 production / 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 interleukin-12 production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / regulation of interleukin-6 production / Signal regulatory protein family interactions / thrombospondin receptor activity / tertiary granule membrane / negative regulation of interleukin-6 production / ficolin-1-rich granule membrane / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / Integrin cell surface interactions / cellular response to interleukin-1 / specific granule membrane / positive regulation of phagocytosis / positive regulation of stress fiber assembly / protein tyrosine kinase binding / negative regulation of protein phosphorylation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / negative regulation of ERK1 and ERK2 cascade / cellular response to hydrogen peroxide / SH3 domain binding / negative regulation of inflammatory response / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of T cell activation / 遊走 / 遺伝子発現の調節 / protein phosphatase binding / 血管新生 / cellular response to lipopolysaccharide / 細胞接着 / 炎症 / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / 細胞膜 / extracellular exosome / 生体膜 / 細胞膜 類似検索 - 分子機能 | |||||||||
生物種 | HOMO SAPIENS (ヒト) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.85 Å | |||||||||
データ登録者 | Hatherley, D. / Graham, S.C. / Turner, J. / Harlos, K. / Stuart, D.I. / Barclay, A.N. | |||||||||
引用 | ジャーナル: Mol. Cell / 年: 2008 タイトル: Paired receptor specificity explained by structures of signal regulatory proteins alone and complexed with CD47. 著者: Hatherley, D. / Graham, S.C. / Turner, J. / Harlos, K. / Stuart, D.I. / Barclay, A.N. | |||||||||
履歴 |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | |||||||||
Remark 700 | 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. |
-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 | 2jjs.cif.gz | 206.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2jjs.ent.gz | 165.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2jjs.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/jj/2jjs ftp://data.pdbj.org/pub/pdb/validation_reports/jj/2jjs | 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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1 |
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2 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 13919.563 Da / 分子数: 2 / 断片: N-TERMINAL ECTODOMAIN, RESIDUES 31-148 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PEE14 / 細胞株 (発現宿主): CHO 発現宿主: CRICETULUS GRISEUS (モンゴルキヌゲネズミ) Variant (発現宿主): LEC3.2.8.1 / 参照: UniProt: P78324 #2: 抗体 | 分子量: 14518.302 Da / 分子数: 2 断片: IMMUNOGLOBULIN-SUPERFAMILY ECTODOMAIN, RESIDUES 19-136 Mutation: YES / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PEE14 / 細胞株 (発現宿主): CHO 発現宿主: CRICETULUS GRISEUS (モンゴルキヌゲネズミ) Variant (発現宿主): LEC3.2.8.1 / 参照: UniProt: Q08722 #3: 糖 | ChemComp-NAG / #4: 化合物 | ChemComp-IOD / #5: 水 | ChemComp-HOH / | 構成要素の詳細 | ENGINEERED | 配列の詳細 | SIRP ALPHA (CHAINS A AND B) RESIDUE NUMBERING IS FOR THE MATURE PROTEIN (LACKING N-TERMINAL 30 ...SIRP ALPHA (CHAINS A AND B) RESIDUE NUMBERING IS FOR THE MATURE PROTEIN (LACKING N-TERMINAL 30 AMINO ACID SIGNAL SEQUENCE). C-TERMINAL PURIFICATI | |
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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: 1 |
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-試料調製
結晶 | マシュー密度: 2.4 Å3/Da / 溶媒含有率: 49.3 % / 解説: NONE |
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結晶化 | 温度: 278 K / pH: 7.4 詳細: 100 NL SIRP ALPHA / CD47 COMPLEX (1:1 RATIO, EACH PROTEIN AT APPROX. 0.375 UM) PLUS 100 NL RESERVOIR (0.2 M POTASSIUM IODIDE, 20% W/V PEG 3350) EQUILIBRATED AGAINST 95 UL OF RESERVOIR AT 5 C., pH 7.4 |
-データ収集
回折 |
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放射光源 |
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検出器 |
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放射 |
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放射波長 |
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反射 | 解像度: 1.85→29.8 Å / Num. obs: 46373 / % possible obs: 100 % / Observed criterion σ(I): -3 / 冗長度: 10.3 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.6 | ||||||||||||||||||
反射 シェル | 解像度: 1.85→1.92 Å / 冗長度: 9.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 2UV3 FOR CHAINS A AND B, PDB ENTRY 2ICC FOR CHAINS C AND D 解像度: 1.85→89.44 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.986 / SU ML: 0.085 / 交差検証法: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.125 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B VALUES INCLUDE TLS CONTRIBUTIONS.
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 20.2 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.85→89.44 Å
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拘束条件 |
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