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基本情報
登録情報 | データベース: EMDB / ID: EMD-2281 | |||||||||
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タイトル | Three-dimensional reconstruction of intact human integrin alphaIIbbeta3 in a phospholipid bilayer nanodisc | |||||||||
![]() | Reconstruction of integrin alphaIIbbeta3 in lipid bilayer nanodisc | |||||||||
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![]() | integrin / alphaIIbbeta3 / nanodisc | |||||||||
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 / fibrinogen binding / maintenance of postsynaptic specialization structure / 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 / angiogenesis involved in wound healing / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / 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 / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / positive regulation of cell adhesion mediated by integrin / wound healing, spreading of epidermal cells / 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 / negative chemotaxis / cell adhesion mediated by integrin / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / activation of protein kinase activity / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / 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 / platelet-derived growth factor receptor signaling pathway / negative regulation of lipid storage / 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 / platelet aggregation / ruffle membrane / 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 | 単粒子再構成法 / ネガティブ染色法 / 解像度: 20.5 Å | |||||||||
![]() | Choi WS / Rice WJ / Stokes DL / Coller BS | |||||||||
![]() | ![]() 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 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 8.5 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 14.3 KB 14.3 KB | 表示 表示 | ![]() |
画像 | ![]() | 45.9 KB | ||
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-検証レポート
文書・要旨 | ![]() | 206.4 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 205.5 KB | 表示 | |
XML形式データ | ![]() | 5.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of integrin alphaIIbbeta3 in lipid bilayer nanodisc | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.96 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
-全体 : Integrin alphaIIbbeta3 in lipid bilayer nanodisc
全体 | 名称: Integrin alphaIIbbeta3 in lipid bilayer nanodisc |
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要素 |
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-超分子 #1000: Integrin alphaIIbbeta3 in lipid bilayer nanodisc
超分子 | 名称: Integrin alphaIIbbeta3 in lipid bilayer nanodisc / タイプ: sample / ID: 1000 / 詳細: The sample was monodisperse. / 集合状態: monomer / Number unique components: 2 |
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分子量 | 実験値: 230 KDa / 理論値: 230 KDa / 手法: SDS-Page |
-分子 #1: integrin alphaIIb
分子 | 名称: integrin alphaIIb / タイプ: protein_or_peptide / ID: 1 / Name.synonym: GPIIb 詳細: Native protein purified from platelet, heterodimer with integrin beta3 subunit コピー数: 1 / 集合状態: hetero dimer / 組換発現: No |
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由来(天然) | 生物種: ![]() |
分子量 | 実験値: 130 KDa / 理論値: 130 KDa |
配列 | UniProtKB: Integrin alpha-IIb |
-分子 #2: Integrin beta3
分子 | 名称: Integrin beta3 / タイプ: protein_or_peptide / ID: 2 / Name.synonym: GPIIIa 詳細: Native protein purified from platelet, heterodimer with integrin alphaIIb subunit コピー数: 1 / 集合状態: hetero dimer / 組換発現: No |
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由来(天然) | 生物種: ![]() |
分子量 | 実験値: 100 KDa / 理論値: 100 KDa |
配列 | UniProtKB: Integrin beta-3 |
-実験情報
-構造解析
手法 | ネガティブ染色法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.025 mg/mL |
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緩衝液 | pH: 7.4 詳細: 150 mM NaCl, 10 mM HEPES, pH 7.4, 1 mM CaCl2 and 1 mM MgCl2 |
染色 | タイプ: NEGATIVE / 詳細: 2% uranyl acetate |
グリッド | 詳細: 200 mesh copper grid with thin carbon support, glow discharged in H2/O2 atmosphere in plasma cleaner |
凍結 | 凍結剤: NONE / 装置: OTHER |
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電子顕微鏡法 #1
Microscopy ID | 1 |
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顕微鏡 | FEI TECNAI F20 |
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 250,000 times magnification |
詳細 | Low dose package used. CCD magnification is ~1.76 times film magnification |
日付 | 2010年2月1日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GENERIC TVIPS (4k x 4k) デジタル化 - サンプリング間隔: 15 µm / 実像数: 1500 / 平均電子線量: 13 e/Å2 / ビット/ピクセル: 16 |
Tilt angle min | 0 |
電子線 | 加速電圧: 120 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 50592 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.0 mm / 最大 デフォーカス(公称値): 1.2 µm / 最小 デフォーカス(公称値): 1.2 µm / 倍率(公称値): 29000 |
試料ステージ | 試料ホルダーモデル: SIDE ENTRY, EUCENTRIC / Tilt angle max: 50 |
実験機器 | ![]() モデル: Tecnai F20 / 画像提供: FEI Company |
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電子顕微鏡法 #2
Microscopy ID | 2 |
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顕微鏡 | FEI TECNAI F20 |
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 250,000 times magnification |
詳細 | Low dose package used. CCD magnification is ~1.76 times film magnification |
日付 | 2010年7月31日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GENERIC TVIPS (4k x 4k) デジタル化 - サンプリング間隔: 15 µm / 実像数: 1500 / 平均電子線量: 13 e/Å2 / ビット/ピクセル: 16 |
Tilt angle min | 0 |
電子線 | 加速電圧: 200 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 88249 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.0 mm / 最大 デフォーカス(公称値): 0.6 µm / 最小 デフォーカス(公称値): 0.6 µm / 倍率(公称値): 50000 |
試料ステージ | 試料ホルダーモデル: SIDE ENTRY, EUCENTRIC / Tilt angle max: 50 |
実験機器 | ![]() モデル: Tecnai F20 / 画像提供: FEI Company |
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画像解析
詳細 | 5 random conical tilt reconstructions were made from class averages, then aligned and merged to make an initial model for reference-based alignment. |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 20.5 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: spider 詳細: Initial model was made from aligning and averaging 5 models made by random conical tilt. 使用した粒子像数: 25008 |
最終 角度割当 | 詳細: SPIDER: theta 45 degrees, phi 45 degrees |
最終 2次元分類 | クラス数: 5 |
-原子モデル構築 1
初期モデル | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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ソフトウェア | 名称: ![]() |
詳細 | The individual alphaIIb and beta3 domains were docked into the anchor graph of the EM map so as to maintain the sequence of domains and the distances between domains in the crystal structure. The locations were then optimized by maximizing the cross-correlation and the atomic inclusion of the domain within the EM map. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: Cross correlation |
得られたモデル | ![]() PDB-4cak: |