+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-31753 | |||||||||||||||
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タイトル | Cryo-EM structure of Patched in lipid nanodisc - the wildtype, 3.5 angstrom (re-processed with dataset of 7dzq) | |||||||||||||||
マップデータ | ||||||||||||||||
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 / caveola / neural tube closure / 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) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | |||||||||||||||
データ登録者 | Luo Y / Zhao Y / Qu Q / Li D | |||||||||||||||
資金援助 | 中国, 4件
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引用 | ジャーナル: Structure / 年: 2021 タイトル: Cryo-EM study of patched in lipid nanodisc suggests a structural basis for its clustering in caveolae. 著者: Yitian Luo / Guoyue Wan / Xiang Zhang / Xuan Zhou / Qiuwen Wang / Jialin Fan / Hongmin Cai / Liya Ma / Hailong Wu / Qianhui Qu / Yao Cong / Yun Zhao / Dianfan Li / 要旨: The 12-transmembrane protein Patched (Ptc1) acts as a suppressor for Hedgehog (Hh) signaling by depleting sterols in the cytoplasmic membrane leaflet that are required for the activation of ...The 12-transmembrane protein Patched (Ptc1) acts as a suppressor for Hedgehog (Hh) signaling by depleting sterols in the cytoplasmic membrane leaflet that are required for the activation of downstream regulators. The positive modulator Hh inhibits Ptc1's transporter function by binding to Ptc1 and its co-receptors, which are locally concentrated in invaginated microdomains known as caveolae. Here, we reconstitute the mouse Ptc1 into lipid nanodiscs and determine its structure using single-particle cryoelectron microscopy. The structure is overall similar to those in amphipol and detergents but displays various conformational differences in the transmembrane region. Although most particles show monomers, we observe Ptc1 dimers with distinct interaction patterns and different membrane curvatures, some of which are reminiscent of caveolae. We find that an extramembranous "hand-shake" region rich in hydrophobic and aromatic residues mediates inter-Ptc1 interactions under different membrane curvatures. Our data provide a plausible framework for Ptc1 clustering in the highly curved caveolae. | |||||||||||||||
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_31753.map.gz | 52.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-31753-v30.xml emd-31753.xml | 17.7 KB 17.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_31753.png | 37.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-31753 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31753 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_31753_validation.pdf.gz | 396.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_31753_full_validation.pdf.gz | 396.3 KB | 表示 | |
XML形式データ | emd_31753_validation.xml.gz | 6.3 KB | 表示 | |
CIF形式データ | emd_31753_validation.cif.gz | 7.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31753 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31753 | 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_31753.map.gz / 形式: CCP4 / 大きさ: 70.2 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: 0.82 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 : Ptc1 in lipid nanodisc
全体 | 名称: Ptc1 in lipid nanodisc |
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要素 |
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-超分子 #1: Ptc1 in lipid nanodisc
超分子 | 名称: Ptc1 in lipid nanodisc / タイプ: complex / ID: 1 / 親要素: 0 / 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) |
分子量 | 実験値: 160 kDa/nm |
-分子 #1: Protein patched homolog 1,Protein patched homolog 1
分子 | 名称: Protein patched homolog 1,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: 121.637617 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MGSASAGNAA GALGRQAGGG RRRRTGGPHR AAPDRDYLHR PSYCDAAFAL EQISKGKATG RKAPLWLRAK FQRLLFKLGC YIQKNCGKF LVVGLLIFGA FAVGLKAANL ETNVEELWVE VGGRVSRELN YTRQKIGEEA MFNPQLMIQT PKEEGANVLT T EALLQHLD ...文字列: MGSASAGNAA GALGRQAGGG RRRRTGGPHR AAPDRDYLHR PSYCDAAFAL EQISKGKATG RKAPLWLRAK FQRLLFKLGC YIQKNCGKF LVVGLLIFGA FAVGLKAANL ETNVEELWVE VGGRVSRELN YTRQKIGEEA MFNPQLMIQT PKEEGANVLT T EALLQHLD SALQASRVHV YMYNRQWKLE HLCYKSGELI TETGYMDQII EYLYPCLIIT PLDCFWEGAK LQSGTAYLLG KP PLRWTNF DPLEFLEELK KINYQVDSWE EMLNKAEVGH GYMDRPCLNP ADPDCPATAP NKNSTKPLDV ALVLNGGCQG LSR KYMHWQ EELIVGGTVK NATGKLVSAH ALQTMFQLMT PKQMYEHFRG YDYVSHINWN EDRAAAILEA WQRTYVEVVH QSVA PNSTQ KVLPFTTTTL DDILKSFSDV SVIRVASGYL LMLAYACLTM LRWDCSKSQG AVGLAGVLLV ALSVAAGLGL CSLIG ISFN AATTQVLPFL ALGVGVDDVF LLAHAFSETG QNKRIPFEDR TGECLKRTGA SVALTSISNV TAFFMAALIP IPALRA FSL QAAVVVVFNF AMVLLIFPAI LSMDLYRRED RRLDIFCCFT SPCVSRVIQV EPQEPPCTKW TLSSFAEKHY APFLLKP KA KVVVILLFLG LLGVSLYGTT RVRDGLDLTD IVPRETREYD FIAAQFKYFS FYNMYIVTQK ADYPNIQHLL YDLHKSFS N VKYVMLEENK QLPQMWLHYF RDWLQGLQDA FDSDWETGRI MPNNYKNGSD DGVLAYKLLV QTGSRDKPID ISQLTKQRL VDADGIINPS AFYIYLTAWV SNDPVAYAAS QANIRPHRPE WVHDKADYMP ETRLRIPAAE PIEYAQFPFY LNGLRDTSDF VEAIEKVRV ICNNYTSLGL SSYPNGYPFL FWEQYISLRH WLLLSISVVL ACTFLVCAVF LLNPWTAGII VMVLALMTVE L FGMMGLIG IKLSAVPVVI LIASVGIGVE FTVHVALAFL TAIGDKNHRA MLALEHMFAP VLDGAVSTLL GVLMLAGSEF DF IVRYFFA VLAILTVLGV LNGLVLLPVL LSFFGPCPEV SPANGTLEVL FQG |
-分子 #3: CHOLESTEROL
分子 | 名称: CHOLESTEROL / タイプ: ligand / ID: 3 / コピー数: 2 / 式: CLR |
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分子量 | 理論値: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-分子 #4: (2S)-2-azanyl-3-[[(2S)-3-butanoyloxy-2-dec-9-enoyloxy-propoxy]-ox...
分子 | 名称: (2S)-2-azanyl-3-[[(2S)-3-butanoyloxy-2-dec-9-enoyloxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid タイプ: ligand / ID: 4 / コピー数: 1 / 式: 5VI |
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分子量 | 理論値: 481.474 Da |
Chemical component information | ChemComp-5VI: |
-分子 #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
分子 | 名称: 2-acetamido-2-deoxy-beta-D-glucopyranose / タイプ: ligand / ID: 5 / コピー数: 3 / 式: NAG |
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分子量 | 理論値: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-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 | 8.5 mg/mL | ||||||||||||||||||
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緩衝液 | pH: 7.5 構成要素:
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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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撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / デジタル化 - サイズ - 横: 5760 pixel / デジタル化 - サイズ - 縦: 4092 pixel / 撮影したグリッド数: 1 / 平均露光時間: 2.23 sec. / 平均電子線量: 60.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 最大 デフォーカス(補正後): 3.0 µm / 最小 デフォーカス(補正後): 1.1 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.2 µm / 最小 デフォーカス(公称値): 1.5 µm / 倍率(公称値): 120000 |
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 |