+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7k65 | ||||||||||||
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タイトル | Hedgehog receptor Patched (PTCH1) in complex with conformation selective nanobody TI23 | ||||||||||||
要素 |
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キーワード | MEMBRANE PROTEIN | ||||||||||||
機能・相同性 | 機能・相同性情報 Ligand-receptor interactions / Activation of SMO / neural plate axis specification / cell differentiation involved in kidney development / hedgehog receptor activity / response to chlorate / cell proliferation involved in metanephros development / smoothened binding / neural tube formation / hedgehog family protein binding ...Ligand-receptor interactions / Activation of SMO / neural plate axis specification / cell differentiation involved in kidney development / hedgehog receptor activity / response to chlorate / cell proliferation involved in metanephros development / smoothened binding / neural tube formation / hedgehog family protein binding / hindlimb morphogenesis / Hedgehog 'on' state / epidermal cell fate specification / spinal cord motor neuron differentiation / prostate gland development / Hedgehog 'off' state / somite development / patched binding / negative regulation of cell division / cellular response to cholesterol / dorsal/ventral neural tube patterning / smooth muscle tissue development / pattern specification process / pharyngeal system development / mammary gland epithelial cell differentiation / mammary gland duct morphogenesis / mammary gland development / cell fate determination / commissural neuron axon guidance / metanephric collecting duct development / dorsal/ventral pattern formation / regulation of growth / embryonic limb morphogenesis / negative regulation of multicellular organism growth / branching involved in ureteric bud morphogenesis / cholesterol binding / positive regulation of epidermal cell differentiation / dendritic growth cone / keratinocyte proliferation / spermatid development / positive regulation of cholesterol efflux / epidermis development / negative regulation of keratinocyte proliferation / negative regulation of osteoblast differentiation / embryonic organ development / axonal growth cone / negative regulation of smoothened signaling pathway / heart morphogenesis / response to mechanical stimulus / response to retinoic acid / negative regulation of stem cell proliferation / regulation of mitotic cell cycle / cyclin binding / epithelial cell proliferation / stem cell proliferation / neural tube closure / caveola / protein localization to plasma membrane / liver regeneration / animal organ morphogenesis / brain development / protein processing / cilium / negative regulation of epithelial cell proliferation / regulation of protein localization / apical part of cell / response to estradiol / glucose homeostasis / heparin binding / regulation of cell population proliferation / midbody / in utero embryonic development / response to xenobiotic stimulus / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / protein-containing complex binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / signal transduction / zinc ion binding / extracellular region / plasma membrane 類似検索 - 分子機能 | ||||||||||||
生物種 | Mus musculus (ハツカネズミ) Lama glama (ラマ) | ||||||||||||
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: 3.4 Å | ||||||||||||
データ登録者 | Zhang, Y. / Bulkley, D.P. / Liang, J. / Manglik, A. / Cheng, Y. / Beachy, P.A. | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2020 タイトル: Hedgehog pathway activation through nanobody-mediated conformational blockade of the Patched sterol conduit. 著者: Yunxiao Zhang / Wan-Jin Lu / David P Bulkley / Jiahao Liang / Arthur Ralko / Shuo Han / Kelsey J Roberts / Anping Li / Wonhwa Cho / Yifan Cheng / Aashish Manglik / Philip A Beachy / 要旨: Activation of the Hedgehog pathway may have therapeutic value for improved bone healing, taste receptor cell regeneration, and alleviation of colitis or other conditions. Systemic pathway activation, ...Activation of the Hedgehog pathway may have therapeutic value for improved bone healing, taste receptor cell regeneration, and alleviation of colitis or other conditions. Systemic pathway activation, however, may be detrimental, and agents amenable to tissue targeting for therapeutic application have been lacking. We have developed an agonist, a conformation-specific nanobody against the Hedgehog receptor Patched1 (PTCH1). This nanobody potently activates the Hedgehog pathway in vitro and in vivo by stabilizing an alternative conformation of a Patched1 "switch helix," as revealed by our cryogenic electron microscopy structure. Nanobody-binding likely traps Patched in one stage of its transport cycle, thus preventing substrate movement through the Patched1 sterol conduit. Unlike the native Hedgehog ligand, this nanobody does not require lipid modifications for its activity, facilitating mechanistic studies of Hedgehog pathway activation and the engineering of pathway activating agents for therapeutic use. Our conformation-selective nanobody approach may be generally applicable to the study of other PTCH1 homologs. | ||||||||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7k65.cif.gz | 215.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7k65.ent.gz | 168.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7k65.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
文書・要旨 | 7k65_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7k65_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | 7k65_validation.xml.gz | 44.2 KB | 表示 | |
CIF形式データ | 7k65_validation.cif.gz | 63.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/k6/7k65 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/7k65 | HTTPS FTP |
-関連構造データ
関連構造データ | 22689MC 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 (文献) |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10328 (タイトル: Hedgehog receptor Patched (PTCH1) in complex with a conformation selective nanobody TI23 Data size: 75.2 Data #1: Particle stack of Hedgehog receptor PTCH1 in complex with nanobody TI23 for final reconstruction [picked particles - multiframe - processed]) |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 142619.938 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Ptch1, Ptch / 細胞株 (発現宿主): freestyle 293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q61115 | ||||
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#2: 抗体 | 分子量: 13821.417 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Lama glama (ラマ) 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) | ||||
#3: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||||
#4: 糖 | ChemComp-NAG / #5: 化合物 | ChemComp-Q7G / 研究の焦点であるリガンドがあるか | N | |
-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 |
-試料調製
構成要素 |
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分子量 | 実験値: NO | ||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 8 | ||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 4.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
試料支持 | グリッドのタイプ: Quantifoil | ||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 298 K |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 12 sec. / 電子線照射量: 85.6 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 実像数: 7046 |
画像スキャン | 横: 3838 / 縦: 3710 / 動画フレーム数/画像: 60 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 3621265 詳細: Particles were picked first using a Gaussian blob as the template and then were re-picked using the 2D classes generated from the first round. | ||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 307652 / アルゴリズム: BACK PROJECTION / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL | ||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 6MG8 PDB chain-ID: A | ||||||||||||||||||||||||||||||||||||
精密化 | 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: 135.37 Å2 | ||||||||||||||||||||||||||||||||||||
拘束条件 |
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