+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2vdn | ||||||||||||
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タイトル | Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist Eptifibatide | ||||||||||||
要素 |
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キーワード | CELL ADHESION/IMMUNE SYSTEM / CELL ADHESION-IMMUNE SYSTEM COMPLEX / FIBRINOGEN BINDING (フィブリノゲン) / PLATELET INTEGRIN ALPHAIIBBETA3 / GLYCOPROTEIN (糖タンパク質) / CELL ADHESION (細胞接着) / MEMBRANE (生体膜) / INTEGRIN (インテグリン) / RECEPTOR (受容体) / ANTAGONIST (受容体拮抗薬) / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID (ピログルタミン酸) / TRANSMEMBRANE (膜貫通型タンパク質) / PHOSPHORYLATION (リン酸化) / DISEASE MUTATION / CLEAVAGE ON PAIR OF BASIC RESIDUES | ||||||||||||
機能・相同性 | 機能・相同性情報 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 / cell-substrate junction assembly / mesodermal cell differentiation / 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 / Syndecan interactions / negative chemotaxis / 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 / 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 / 着床 / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / Signal transduction by L1 / response to activity / 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 / 凝固・線溶系 / 血小板 / ruffle membrane / VEGFA-VEGFR2 Pathway / 細胞接着 / 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 | HOMO SAPIENS (ヒト) MUS MUSCULUS (ハツカネズミ) SYNTHETIC CONSTRUCT (人工物) | ||||||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.9 Å | ||||||||||||
データ登録者 | Springer, T.A. / Zhu, J. / Xiao, T. | ||||||||||||
引用 | ジャーナル: J.Cell Biol. / 年: 2008 タイトル: Structural Basis for Distinctive Recognition of Fibrinogen Gammac Peptide by the Platelet Integrin Alphaiibbeta3. 著者: Springer, T.A. / Zhu, J. / Xiao, T. #1: ジャーナル: Nature / 年: 2004 タイトル: Structural Basis for Allostery in Integrins and Binding to Fibrinogen-Mimetic Therapeutics 著者: Xiao, T. / Takagi, J. / Coller, B.S. / Wang, J.-H. / Springer, T.A. | ||||||||||||
履歴 |
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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 | 2vdn.cif.gz | 293.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2vdn.ent.gz | 231.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2vdn.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/vd/2vdn ftp://data.pdbj.org/pub/pdb/validation_reports/vd/2vdn | 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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単位格子 |
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-要素
-タンパク質 , 2種, 2分子 AB
#1: タンパク質 | 分子量: 49030.367 Da / 分子数: 1 / 断片: HEADPIECE, RESIDUES 32-483 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 細胞株 (発現宿主): LEC 3.2.8.1 発現宿主: CRICETULUS GRISEUS (モンゴルキヌゲネズミ) 参照: UniProt: P08514 |
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#2: タンパク質 | 分子量: 50969.664 Da / 分子数: 1 / 断片: HEADPIECE, RESIDUES 27-487 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 細胞株 (発現宿主): LEC 3.2.8.1 発現宿主: CRICETULUS GRISEUS (モンゴルキヌゲネズミ) 参照: UniProt: P05106 |
-タンパク質・ペプチド , 1種, 1分子 C
#3: タンパク質・ペプチド | 分子量: 832.972 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) SYNTHETIC CONSTRUCT (人工物) |
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-抗体 , 2種, 2分子 HL
#4: 抗体 | 分子量: 23766.473 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) MUS MUSCULUS (ハツカネズミ) / 細胞株: 10E5 HYBRIDOMA / 株: BALB/C |
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#5: 抗体 | 分子量: 23332.686 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) MUS MUSCULUS (ハツカネズミ) / 細胞株: 10E5 HYBRIDOMA / 株: BALB/C |
-糖 , 3種, 5分子
#6: 多糖 | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#7: 多糖 | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#10: 糖 |
-非ポリマー , 4種, 373分子
#8: 化合物 | #9: 化合物 | ChemComp-CA / #11: 化合物 | ChemComp-MG / | #12: 水 | ChemComp-HOH / | |
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-詳細
配列の詳細 | ACCORDING TO THE AUTHORS THE CORRECT CHAIN A SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 88758615 WHICH ...ACCORDING TO THE AUTHORS THE CORRECT CHAIN A SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 88758615 WHICH SHOULD BE USED IN PLACE OF P08514. |
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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: 3.8 Å3/Da / 溶媒含有率: 67.2 % / 解説: NONE |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: 11% PEG 3350, 0.7 M MAGNESIUM ACETATE, 0.1 M IMIDAZOLE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: CHESS / ビームライン: A1 / 波長: 0.976 |
検出器 | タイプ: ADSC CCD / 検出器: CCD / 日付: 2003年10月4日 / 詳細: MIRROR |
放射 | モノクロメーター: RH-COATED SI / 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 | 波長: 0.976 Å / 相対比: 1 |
反射 | 解像度: 2.9→50 Å / Num. obs: 50647 / % possible obs: 100 % / Observed criterion σ(I): 0 / 冗長度: 7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.9 |
反射 シェル | 解像度: 2.9→3 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.7 / % 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 1TXV 1txv 解像度: 2.9→47.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / SU B: 22.178 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 1.054 / ESU R Free: 0.311 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THESE ARE RE-REFINED COORDINATES OF THE PREVIOUS WWPDB SUBMISSION 1TY6. THE STARTING MODEL WAS A 2.4 ANGSTROM STRUCTURE WITH A DIFFERENT ...詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THESE ARE RE-REFINED COORDINATES OF THE PREVIOUS WWPDB SUBMISSION 1TY6. THE STARTING MODEL WAS A 2.4 ANGSTROM STRUCTURE WITH A DIFFERENT BOUND LIGAND. THE MODEL IS REFINED TO LOWER RFREE. ONE SEQUENCE MISTAKE IN THE AIIB SUBUNIT IS CORRECTED. MORE OF BETA SUBUNIT DOMAIN I-EGF1 IS BUILT. MISTAKES IN CARBOHYDRATE ANOMERIC LINKAGES ARE ALSO CORRECTED.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 44.6 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.9→47.19 Å
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拘束条件 |
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