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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 9ckv | |||||||||||||||
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タイトル | Cryo-EM structure of alpha5beta1 integrin in complex with NeoNectin | |||||||||||||||
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![]() | SIGNALING PROTEIN / a5B1 / de novo / tissue regeneration / extracellular matrix protein | |||||||||||||||
機能・相同性 | ![]() integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process ...integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process / integrin alpha9-beta1 complex / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / C-X3-C chemokine binding / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of synapse pruning / reactive gliosis / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / Formation of the ureteric bud / CD40 signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / basement membrane organization / myelin sheath abaxonal region / alphav-beta3 integrin-vitronectin complex / CHL1 interactions / cardiac muscle cell myoblast differentiation / Laminin interactions / RUNX2 regulates genes involved in cell migration / MET interacts with TNS proteins / germ cell migration / leukocyte tethering or rolling / cardiac muscle cell differentiation / cell projection organization / Platelet Adhesion to exposed collagen / vascular endothelial growth factor receptor 2 binding / myoblast fusion / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / platelet-derived growth factor receptor binding / axon extension / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / cell migration involved in sprouting angiogenesis / wound healing, spreading of epidermal cells / regulation of spontaneous synaptic transmission / heterotypic cell-cell adhesion / myoblast differentiation / integrin complex / positive regulation of cell-substrate adhesion / dendrite morphogenesis / Basigin interactions / Molecules associated with elastic fibres / muscle organ development / negative regulation of Rho protein signal transduction / lamellipodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / MET activates PTK2 signaling / cell adhesion mediated by integrin / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / Syndecan interactions / epidermal growth factor receptor binding / positive regulation of wound healing / maintenance of blood-brain barrier / sarcomere organization / positive regulation of neuroblast proliferation / cell-substrate adhesion / positive regulation of sprouting angiogenesis / endodermal cell differentiation / TGF-beta receptor signaling activates SMADs / homophilic cell adhesion via plasma membrane adhesion molecules / establishment of mitotic spindle orientation / glial cell projection / cleavage furrow / fibronectin binding / cellular response to low-density lipoprotein particle stimulus / negative regulation of anoikis / intercalated disc / RHOG GTPase cycle / negative regulation of neuron differentiation / ECM proteoglycans / neuroblast proliferation / RAC2 GTPase cycle / RAC3 GTPase cycle / Integrin cell surface interactions / cellular defense response / coreceptor activity / phagocytosis 類似検索 - 分子機能 | |||||||||||||||
生物種 | ![]() synthetic construct (人工物) | |||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.19 Å | |||||||||||||||
![]() | Werther, R. / Nguyen, A. / Estrada Alamo, K.A. / Wang, X. / Campbell, M.G. | |||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: De Novo Design of Integrin alpha5beta1 Modulating Proteins for Regenerative Medicine 著者: Wang, X. / Guillem-Marti, J. / Kumar, S. / Lee, D.S. / Cabrerizo-Aguado, D. / Werther, R. / Estrada Alamo, K.A. / Zhao, Y.T. / Nguyen, A. / Kopyeva, I. / Huang, B. / Li, J. / Hao, Y. / Li, X. ...著者: Wang, X. / Guillem-Marti, J. / Kumar, S. / Lee, D.S. / Cabrerizo-Aguado, D. / Werther, R. / Estrada Alamo, K.A. / Zhao, Y.T. / Nguyen, A. / Kopyeva, I. / Huang, B. / Li, J. / Hao, Y. / Li, X. / Brizuela-Velasco, A. / Murray, A.N. / Gerben, S. / Roy, A. / DeForest, C.A. / Springer, T. / Ruohola-Baker, H. / Cooper, J.A. / Campbell, M.G. / Maria Manero, J. / Ginebra, M. / Baker, D. | |||||||||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 326 KB | 表示 | ![]() |
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PDB形式 | ![]() | 246.4 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 | ![]() | 1.8 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.8 MB | 表示 | |
XML形式データ | ![]() | 42.6 KB | 表示 | |
CIF形式データ | ![]() | 62.3 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 45655MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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要素
-タンパク質 , 3種, 3分子 ABC
#1: タンパク質 | 分子量: 109695.867 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P08648 |
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#2: タンパク質 | 分子量: 81743.961 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P05556 |
#3: タンパク質 | 分子量: 11270.766 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: ![]() ![]() |
-糖 , 4種, 8分子 ![](data/chem/img/NAG.gif)
#4: 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 | ||||
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#5: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #6: 多糖 | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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 | #8: 糖 | |
-非ポリマー , 2種, 7分子 ![](data/chem/img/CA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/MN.gif)
#7: 化合物 | ChemComp-CA / #9: 化合物 | |
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-詳細
研究の焦点であるリガンドがあるか | N |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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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 |
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試料調製
構成要素 | 名称: Protein complex of wild type integrin alpha-5 beta-1 with computationally designed protein NeoNectin タイプ: COMPLEX / Entity ID: #1-#3 / 由来: RECOMBINANT | ||||||||||||||||||||
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分子量 | 実験値: NO | ||||||||||||||||||||
由来(天然) | 生物種: ![]() | ||||||||||||||||||||
由来(組換発現) | 生物種: ![]() ![]() | ||||||||||||||||||||
緩衝液 | pH: 7.4 | ||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
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電子顕微鏡撮影
顕微鏡 | モデル: TFS GLACIOS |
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電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 36000 X / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 1200 nm / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 3 / 詳細: Collection at 30 degrees tilt |
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解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3次元再構成 | 解像度: 3.19 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 72604 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 131.55 Å2 | ||||||||||||||||||||||||
拘束条件 |
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