+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 4cak | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Three-dimensional reconstruction of intact human integrin alphaIIbbeta3 in a phospholipid bilayer nanodisc | ||||||||||||
![]() |
| ||||||||||||
![]() | CELL ADHESION / INTEGRIN / SINGLE PARTICLE RECONSTRUCTION | ||||||||||||
機能・相同性 | ![]() tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / maintenance of postsynaptic specialization structure / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / glycinergic synapse / negative regulation of low-density lipoprotein receptor activity / regulation of release of sequestered calcium ion into cytosol / angiogenesis involved in wound healing / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of cell adhesion mediated by integrin / heterotypic cell-cell adhesion / integrin complex / Molecules associated with elastic fibres / positive regulation of leukocyte migration / positive regulation of cell-matrix adhesion / cellular response to insulin-like growth factor stimulus / smooth muscle cell migration / microvillus membrane / cell adhesion mediated by integrin / negative chemotaxis / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / activation of protein kinase activity / cellular response to platelet-derived growth factor stimulus / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / platelet-derived growth factor receptor signaling pathway / fibronectin binding / ECM proteoglycans / positive regulation of T cell migration / positive regulation of bone resorption / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / embryo implantation / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / positive regulation of smooth muscle cell proliferation / Signaling by high-kinase activity BRAF mutants / wound healing / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet activation / ruffle membrane / platelet aggregation / VEGFA-VEGFR2 Pathway / cell-cell adhesion / cellular response to mechanical stimulus / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / regulation of protein localization 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / ネガティブ染色法 / 解像度: 20.5 Å | ||||||||||||
![]() | Choi, W.S. / Rice, W.J. / Stokes, D.L. / Coller, B.S. | ||||||||||||
![]() | ![]() タイトル: Three-dimensional reconstruction of intact human integrin αIIbβ3: new implications for activation-dependent ligand binding. 著者: Won-Seok Choi / William J Rice / David L Stokes / Barry S Coller / ![]() 要旨: Integrin αIIbβ3 plays a central role in hemostasis and thrombosis. We provide the first 3-dimensional reconstruction of intact purified αIIbβ3 in a nanodisc lipid bilayer. Unlike previous models, ...Integrin αIIbβ3 plays a central role in hemostasis and thrombosis. We provide the first 3-dimensional reconstruction of intact purified αIIbβ3 in a nanodisc lipid bilayer. Unlike previous models, it shows that the ligand-binding head domain is on top, pointing away from the membrane. Moreover, unlike the crystal structure of the recombinant ectodomain, the lower legs are not parallel, straight, and adjacent. Rather, the αIIb lower leg is bent between the calf-1 and calf-2 domains and the β3 Integrin-Epidermal Growth Factor (I-EGF) 2 to 4 domains are freely coiled rather than in a cleft between the β3 headpiece and the αIIb lower leg. Our data indicate an important role for the region that links the distal calf-2 and β-tail domains to their respective transmembrane (TM) domains in transmitting the conformational changes in the TM domains associated with inside-out activation. | ||||||||||||
履歴 |
|
-
構造の表示
ムービー |
![]() |
---|---|
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 | ![]() | 426.4 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 299.9 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 | ![]() | 1.1 MB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 1.5 MB | 表示 | |
XML形式データ | ![]() | 120 KB | 表示 | |
CIF形式データ | ![]() | 159.3 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 |
|
-
要素
-タンパク質 , 2種, 2分子 AB
#1: タンパク質 | 分子量: 104460.719 Da / 分子数: 1 / 断片: ECTODOMAIN, UNP RESIDUES 32-990 / 由来タイプ: 天然 / 詳細: FITTED FROM PDB ID 3FCS / 由来: (天然) ![]() |
---|---|
#2: タンパク質 | 分子量: 76316.945 Da / 分子数: 1 / 断片: RESIDUES 27-716 / 由来タイプ: 天然 / 詳細: FITTED FROM PDB ID 3FCS / 由来: (天然) ![]() |
-糖 , 5種, 7分子 ![](data/chem/img/NAG.gif)
#3: 多糖 | #4: 多糖 | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #5: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #6: 多糖 | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #7: 糖 | |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-
試料調製
構成要素 | 名称: INTEGRIN ALPHAIIBBETA3 IN LIPID BILAYER NANODISC / タイプ: COMPLEX / 詳細: MICROGRAPHS TAKEN ON CCD |
---|---|
緩衝液 | 名称: 150 MM NACL, 10 MM HEPES, PH 7.4, 1 MM CACL2 AND 1 MM MGCL2 pH: 7.4 詳細: 150 MM NACL, 10 MM HEPES, PH 7.4, 1 MM CACL2 AND 1 MM MGCL2 |
試料 | 濃度: 0.02 mg/ml / 包埋: NO / シャドウイング: NO / 染色: YES / 凍結: NO |
染色 | タイプ: NEGATIVE / 染色剤: uranyl acetate |
試料支持 | 詳細: CARBON |
急速凍結 | 詳細: VITRIFICATION 1 -- CRYOGEN- NONE, INSTRUMENT- NONE, |
-
電子顕微鏡撮影
実験機器 | ![]() モデル: Tecnai F20 / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TECNAI F20 / 日付: 2010年2月1日 詳細: LOW DOSE PACKAGE USED. CCD MAGNIFICATION IS 1.76 TIMES FILM MAGNIFICATION |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 29000 X / 倍率(補正後): 50592 X / 最大 デフォーカス(公称値): 1500 nm / 最小 デフォーカス(公称値): 1200 nm / Cs: 2 mm |
試料ホルダ | 傾斜角・最大: 50 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 13 e/Å2 フィルム・検出器のモデル: GENERIC TVIPS (4k x 4k) |
画像スキャン | デジタル画像の数: 1500 |
放射波長 | 相対比: 1 |
-
解析
EMソフトウェア |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
対称性 | 点対称性: C1 (非対称) | ||||||||||||
3次元再構成 | 手法: RANDOM CONICAL TILT THEN REFERENCE BASED RECONSTRUCTION 解像度: 20.5 Å / 粒子像の数: 25008 / ピクセルサイズ(公称値): 2.96 Å / ピクセルサイズ(実測値): 2.96 Å / 倍率補正: 23A LAYERLINE OF TMV 詳細: INITIAL MODEL FROM RANDOM CONICAL TILT FOLLOWED BY REFERENCE BASED REFINEMENT PDB FILE 3FCS WAS SPLIT INTO 20 SUBDOMAINS. THESE SUBDOMAINS WERE MANUALLY FITTED INTO THE EM VOLUME SUBMISSION ...詳細: INITIAL MODEL FROM RANDOM CONICAL TILT FOLLOWED BY REFERENCE BASED REFINEMENT PDB FILE 3FCS WAS SPLIT INTO 20 SUBDOMAINS. THESE SUBDOMAINS WERE MANUALLY FITTED INTO THE EM VOLUME SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2281. (DEPOSITION ID: 11378). 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL / Target criteria: Cross-correlation coefficient / 詳細: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY | ||||||||||||
原子モデル構築 | PDB-ID: 3FCS | ||||||||||||
精密化 | 最高解像度: 20.5 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 20.5 Å
|