+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-30342 | |||||||||
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タイトル | Structure of alpha6beta1 integrin in complex with laminin-511 | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 laminin-5 complex / laminin-11 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / extracellular matrix of synaptic cleft / laminin-1 complex / laminin-10 complex / integrin alpha6-beta1 complex / integrin alpha8-beta1 complex ...laminin-5 complex / laminin-11 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / extracellular matrix of synaptic cleft / laminin-1 complex / laminin-10 complex / integrin alpha6-beta1 complex / 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 / regulation of basement membrane organization / ectodermal cell differentiation / integrin alpha4-beta1 complex / neuregulin binding / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / cell-cell adhesion mediated by integrin / L1CAM interactions / integrin alpha1-beta1 complex / Type I hemidesmosome assembly / trunk neural crest cell migration / hemidesmosome assembly / nail development / 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 / postsynapse organization / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / positive regulation of integrin-mediated signaling pathway / Formation of the ureteric bud / CD40 signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / morphogenesis of embryonic epithelium / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / morphogenesis of a polarized epithelium / basement membrane organization / myelin sheath abaxonal region / tissue development / CHL1 interactions / cardiac muscle cell myoblast differentiation / Laminin interactions / skin morphogenesis / MET interacts with TNS proteins / EGR2 and SOX10-mediated initiation of Schwann cell myelination / germ cell migration / leukocyte tethering or rolling / endoderm development / cardiac muscle cell differentiation / cell projection organization / branching involved in salivary gland morphogenesis / Platelet Adhesion to exposed collagen / protein complex involved in cell-matrix adhesion / insulin-like growth factor I binding / myoblast fusion / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / regulation of epithelial cell proliferation / axon extension / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / myoblast differentiation / integrin complex / regulation of spontaneous synaptic transmission / dendrite morphogenesis / cellular response to low-density lipoprotein particle stimulus / odontogenesis / Molecules associated with elastic fibres / Basigin interactions / hair follicle development / muscle organ development / lamellipodium assembly / negative regulation of Rho protein signal transduction / cell adhesion mediated by integrin / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / Syndecan interactions / negative regulation of vasoconstriction / branching involved in ureteric bud morphogenesis 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
データ登録者 | Arimori T / Miyazaki N / Takagi J | |||||||||
資金援助 | 日本, 2件
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引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Structural mechanism of laminin recognition by integrin. 著者: Takao Arimori / Naoyuki Miyazaki / Emiko Mihara / Mamoru Takizawa / Yukimasa Taniguchi / Carlos Cabañas / Kiyotoshi Sekiguchi / Junichi Takagi / 要旨: Recognition of laminin by integrin receptors is central to the epithelial cell adhesion to basement membrane, but the structural background of this molecular interaction remained elusive. Here, we ...Recognition of laminin by integrin receptors is central to the epithelial cell adhesion to basement membrane, but the structural background of this molecular interaction remained elusive. Here, we report the structures of the prototypic laminin receptor α6β1 integrin alone and in complex with three-chain laminin-511 fragment determined via crystallography and cryo-electron microscopy, respectively. The laminin-integrin interface is made up of several binding sites located on all five subunits, with the laminin γ1 chain C-terminal portion providing focal interaction using two carboxylate anchor points to bridge metal-ion dependent adhesion site of integrin β1 subunit and Asn189 of integrin α6 subunit. Laminin α5 chain also contributes to the affinity and specificity by making electrostatic interactions with large surface on the β-propeller domain of α6, part of which comprises an alternatively spliced X1 region. The propeller sheet corresponding to this region shows unusually high mobility, suggesting its unique role in ligand capture. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_30342.map.gz | 8.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-30342-v30.xml emd-30342.xml | 25.5 KB 25.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_30342.png | 123.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-30342 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30342 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_30342_validation.pdf.gz | 322.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_30342_full_validation.pdf.gz | 321.9 KB | 表示 | |
XML形式データ | emd_30342_validation.xml.gz | 6.4 KB | 表示 | |
CIF形式データ | emd_30342_validation.cif.gz | 7.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30342 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30342 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_30342.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.113 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
-試料の構成要素
+全体 : Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 F...
+超分子 #1: Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 F...
+分子 #1: Integrin alpha-6
+分子 #2: Integrin beta-1
+分子 #3: Laminin subunit alpha-5
+分子 #4: Laminin subunit beta-1
+分子 #5: Laminin subunit gamma-1
+分子 #6: TS2/16 VH(S112C)-SARAH,TS2/16 VH(S112C)-SARAH
+分子 #7: TS2/16 VL-SARAH(S37C),TS2/16 VL-SARAH(S37C)
+分子 #8: HUTS-4 VH(S112C)-SARAH,HUTS-4 VH(S112C)-SARAH
+分子 #9: HUTS-4 VL(C87Y)-SARAH(S37C),HUTS-4 VL(C87Y)-SARAH(S37C)
+分子 #11: CALCIUM ION
+分子 #12: 2-acetamido-2-deoxy-beta-D-glucopyranose
+分子 #13: MANGANESE (II) ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.07 mg/mL | |||||||||||||||
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緩衝液 | pH: 7.5 構成要素:
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グリッド | モデル: Quantifoil R2/1 / 材質: MOLYBDENUM / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 前処理 - タイプ: GLOW DISCHARGE | |||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | 位相板: VOLTA PHASE PLATE |
撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 検出モード: INTEGRATING / デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / 撮影したグリッド数: 1 / 実像数: 7768 / 平均電子線量: 40.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 0.8 µm / 最小 デフォーカス(公称値): 0.6 µm / 倍率(公称値): 59000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |