+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-22689 | ||||||||||||
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タイトル | Hedgehog receptor Patched (PTCH1) in complex with conformation selective nanobody TI23 | ||||||||||||
マップデータ | Sharpened map of Patched in complex with nanobody TI23 | ||||||||||||
試料 |
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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 | 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 DP / Liang J / Manglik A / Cheng Y / Beachy PA | ||||||||||||
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 | 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_22689.map.gz | 59.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-22689-v30.xml emd-22689.xml | 22.9 KB 22.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_22689.png | 127.3 KB | ||
その他 | emd_22689_half_map_1.map.gz emd_22689_half_map_2.map.gz | 18.3 MB 2.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-22689 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22689 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_22689_validation.pdf.gz | 707.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_22689_full_validation.pdf.gz | 706.7 KB | 表示 | |
XML形式データ | emd_22689_validation.xml.gz | 12.6 KB | 表示 | |
CIF形式データ | emd_22689_validation.cif.gz | 14.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22689 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22689 | HTTPS FTP |
-関連構造データ
関連構造データ | 7k65MC M: このマップから作成された原子モデル 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
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_22689.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened map of Patched in complex with nanobody TI23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.059 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
-ハーフマップ: half map 1
ファイル | emd_22689_half_map_1.map | ||||||||||||
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注釈 | half map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 2
ファイル | emd_22689_half_map_2.map | ||||||||||||
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注釈 | Half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Complex between Hedgehog receptor PTCH1 and nanobody TI23
全体 | 名称: Complex between Hedgehog receptor PTCH1 and nanobody TI23 |
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要素 |
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-超分子 #1: Complex between Hedgehog receptor PTCH1 and nanobody TI23
超分子 | 名称: Complex between Hedgehog receptor PTCH1 and nanobody TI23 タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#2 |
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-超分子 #2: Hedgehog receptor Patched PTCH1
超分子 | 名称: Hedgehog receptor Patched PTCH1 / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1 |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
組換発現 | 生物種: Homo sapiens (ヒト) / 組換細胞: HEK293 |
-超分子 #3: nanobody TI23
超分子 | 名称: nanobody TI23 / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #2 |
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由来(天然) | 生物種: Lama glama (ラマ) |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
-分子 #1: Protein patched homolog 1
分子 | 名称: Protein patched homolog 1 / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 142.619938 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MASAGNAAGA LGRQAGGGRR RRTGGPHRAA PDRDYLHRPS YCDAAFALEQ ISKGKATGRK APLWLRAKFQ RLLFKLGCYI QKNCGKFLV VGLLIFGAFA VGLKAANLET NVEELWVEVG GRVSRELNYT RQKIGEEAMF NPQLMIQTPK EEGANVLTTE A LLQHLDSA ...文字列: MASAGNAAGA LGRQAGGGRR RRTGGPHRAA PDRDYLHRPS YCDAAFALEQ ISKGKATGRK APLWLRAKFQ RLLFKLGCYI QKNCGKFLV VGLLIFGAFA VGLKAANLET NVEELWVEVG GRVSRELNYT RQKIGEEAMF NPQLMIQTPK EEGANVLTTE A LLQHLDSA LQASRVHVYM YNRQWKLEHL CYKSGELITE TGYMDQIIEY LYPCLIITPL DCFWEGAKLQ SGTAYLLGKP PL RWTNFDP LEFLEELKKI NYQVDSWEEM LNKAEVGHGY MDRPCLNPAD PDCPATAPNK NSTKPLDVAL VLNGGCQGLS RKY MHWQEE LIVGGTVKNA TGKLVSAHAL QTMFQLMTPK QMYEHFRGYD YVSHINWNED RAAAILEAWQ RTYVEVVHQS VAPN STQKV LPFTTTTLDD ILKSFSDVSV IRVASGYLLM LAYACLTMLR WDCSKSQGAV GLAGVLLVAL SVAAGLGLCS LIGIS FNAA TTQVLPFLAL GVGVDDVFLL AHAFSETGQN KRIPFEDRTG ECLKRTGASV ALTSISNVTA FFMAALIPIP ALRAFS LQA AVVVVFNFAM VLLIFPAILS MDLYRREDRR LDIFCCFTSP CVSRVIQVEP QAYTEPMQST VQLRTEYDPH THVYYTT AE PRSEISVQPV TVTQDNLSCQ SPESTSSTRD LLSQFSDSSL HCLEPPCTKW TLSSFAEKHY APFLLKPKAK VVVILLFL G LLGVSLYGTT RVRDGLDLTD IVPRETREYD FIAAQFKYFS FYNMYIVTQK ADYPNIQHLL YDLHKSFSNV KYVMLEENK QLPQMWLHYF RDWLQGLQDA FDSDWETGRI MPNNYKNGSD DGVLAYKLLV QTGSRDKPID ISQLTKQRLV DADGIINPSA FYIYLTAWV SNDPVAYAAS QANIRPHRPE WVHDKADYMP ETRLRIPAAE PIEYAQFPFY LNGLRDTSDF VEAIEKVRVI C NNYTSLGL SSYPNGYPFL FWEQYISLRH WLLLSISVVL ACTFLVCAVF LLNPWTAGII VMVLALMTVE LFGMMGLIGI KL SAVPVVI LIASVGIGVE FTVHVALAFL TAIGDKNHRA MLALEHMFAP VLDGAVSTLL GVLMLAGSEF DFIVRYFFAV LAI LTVLGV LNGLVLLPVL LSFFGPCPEV SPANGLNRLP TPSPEPPPSV VRFAVPPGHT NNGSDSSDSE YSSQTTVSGI SEEL RQYEA QQGAGGPAHQ VIVEATENPV FARSTVVHPD SRHQPPLTPR QQPHLDSGSL SPGRQGQQPR RDMDEKTTGW RGGHV V |
-分子 #2: nanobody TI23
分子 | 名称: nanobody TI23 / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Lama glama (ラマ) |
分子量 | 理論値: 13.821417 KDa |
組換発現 | 生物種: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) |
配列 | 文字列: QVQLQESGGG LVQAGGSLRL SCAASGNIFA YYIMGWYRQA PGKERELVAT IDIGGNTNYA DSVKGRFTIS RDNAKNNVYL QMNSLKPED TAVYYCAVQA VPIRYRRYWG QGTQVTVSSH HHHHH |
-分子 #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
分子 | 名称: 2-acetamido-2-deoxy-beta-D-glucopyranose / タイプ: ligand / ID: 4 / コピー数: 5 / 式: NAG |
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分子量 | 理論値: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-分子 #5: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl...
分子 | 名称: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside タイプ: ligand / ID: 5 / コピー数: 4 / 式: Q7G |
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分子量 | 理論値: 1.165315 KDa |
Chemical component information | ChemComp-Q7G: |
-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 | 4.5 mg/mL | ||||||||||||
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緩衝液 | pH: 8 構成要素:
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グリッド | モデル: Quantifoil | ||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 298 K / 装置: FEI VITROBOT MARK III |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / デジタル化 - サイズ - 横: 3838 pixel / デジタル化 - サイズ - 縦: 3710 pixel / 実像数: 7046 / 平均露光時間: 12.0 sec. / 平均電子線量: 85.6 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 |
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 |