+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-25007 | |||||||||
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タイトル | CryoEM structure of the Caveolin-1 8S complex | |||||||||
マップデータ | Refined and sharpened volume of the Caveolin-1 8S complex with applied C11 symmetry | |||||||||
試料 |
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キーワード | caveolin / caveolae / cryoEM / disc / monotopic proteins / STRUCTURAL PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of peptidyl-tyrosine autophosphorylation / receptor internalization involved in canonical Wnt signaling pathway / caveolar macromolecular signaling complex / protein localization to plasma membrane raft / inward rectifier potassium channel inhibitor activity / negative regulation of inward rectifier potassium channel activity / : / regulation of peptidase activity / angiotensin-activated signaling pathway involved in heart process / caveola assembly ...negative regulation of peptidyl-tyrosine autophosphorylation / receptor internalization involved in canonical Wnt signaling pathway / caveolar macromolecular signaling complex / protein localization to plasma membrane raft / inward rectifier potassium channel inhibitor activity / negative regulation of inward rectifier potassium channel activity / : / regulation of peptidase activity / angiotensin-activated signaling pathway involved in heart process / caveola assembly / intracellular nitric oxide homeostasis / protein localization to basolateral plasma membrane / negative regulation of cytokine-mediated signaling pathway / negative regulation of protein tyrosine kinase activity / insulin receptor internalization / cellular response to hyperoxia / regulation of entry of bacterium into host cell / positive regulation of toll-like receptor 3 signaling pathway / regulation of ruffle assembly / negative regulation of nitric-oxide synthase activity / regulation of cardiac muscle cell action potential involved in regulation of contraction / negative regulation of pinocytosis / regulation of membrane repolarization during action potential / negative regulation of potassium ion transmembrane transport / acrosomal membrane / regulation of the force of heart contraction by chemical signal / negative regulation of tyrosine phosphorylation of STAT protein / NOSTRIN mediated eNOS trafficking / FOXO-mediated transcription of cell cycle genes / mammary gland involution / positive regulation of cell adhesion molecule production / basement membrane organization / regulation of fatty acid metabolic process / vesicle organization / regulation of smooth muscle contraction / maintenance of protein location in cell / patched binding / peptidase activator activity / negative regulation of nitric oxide biosynthetic process / lipid storage / negative regulation of receptor signaling pathway via JAK-STAT / mammary gland development / caveolin-mediated endocytosis / regulation of ventricular cardiac muscle cell action potential / vasoconstriction / cholesterol transport / negative regulation of necroptotic process / RHOF GTPase cycle / RHOD GTPase cycle / positive regulation of extrinsic apoptotic signaling pathway / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Basigin interactions / RND1 GTPase cycle / RND2 GTPase cycle / cellular response to peptide hormone stimulus / RND3 GTPase cycle / negative regulation of epithelial cell differentiation / negative regulation of MAPK cascade / post-transcriptional regulation of gene expression / positive regulation of calcium ion transport into cytosol / RHOB GTPase cycle / triglyceride metabolic process / cholesterol binding / positive regulation of catalytic activity / nitric-oxide synthase binding / cellular response to exogenous dsRNA / regulation of cell communication by electrical coupling involved in cardiac conduction / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / Triglyceride catabolism / negative regulation of peptidyl-serine phosphorylation / regulation of heart rate by cardiac conduction / regulation of blood coagulation / plasma membrane => GO:0005886 / negative regulation of endothelial cell proliferation / membrane depolarization / CDC42 GTPase cycle / RHOH GTPase cycle / positive regulation of gap junction assembly / negative regulation of anoikis / negative regulation of BMP signaling pathway / RHOG GTPase cycle / RHOA GTPase cycle / positive regulation of cholesterol efflux / RAC2 GTPase cycle / RAC3 GTPase cycle / vasculogenesis / calcium ion homeostasis / eNOS activation / positive regulation of intrinsic apoptotic signaling pathway / skeletal muscle tissue development / positive regulation of vasoconstriction / negative regulation of protein ubiquitination / cellular response to transforming growth factor beta stimulus / regulation of cytosolic calcium ion concentration / T cell costimulation / RAC1 GTPase cycle / lactation / cellular response to starvation 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: 3.4 Å | |||||||||
データ登録者 | Porta JP / Ohi MD | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Sci Adv / 年: 2022 タイトル: Molecular architecture of the human caveolin-1 complex. 著者: Jason C Porta / Bing Han / Alican Gulsevin / Jeong Min Chung / Yelena Peskova / Sarah Connolly / Hassane S Mchaourab / Jens Meiler / Erkan Karakas / Anne K Kenworthy / Melanie D Ohi / 要旨: Membrane-sculpting proteins shape the morphology of cell membranes and facilitate remodeling in response to physiological and environmental cues. Complexes of the monotopic membrane protein caveolin ...Membrane-sculpting proteins shape the morphology of cell membranes and facilitate remodeling in response to physiological and environmental cues. Complexes of the monotopic membrane protein caveolin function as essential curvature-generating components of caveolae, flask-shaped invaginations that sense and respond to plasma membrane tension. However, the structural basis for caveolin's membrane remodeling activity is currently unknown. Here, we show that, using cryo-electron microscopy, the human caveolin-1 complex is composed of 11 protomers organized into a tightly packed disc with a flat membrane-embedded surface. The structural insights suggest a previously unrecognized mechanism for how membrane-sculpting proteins interact with membranes and reveal how key regions of caveolin-1, including its scaffolding, oligomerization, and intramembrane domains, contribute to its function. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_25007.map.gz | 230 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-25007-v30.xml emd-25007.xml | 15.1 KB 15.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_25007_fsc.xml | 18.3 KB | 表示 | FSCデータファイル |
画像 | emd_25007.png | 211.6 KB | ||
Filedesc metadata | emd-25007.cif.gz | 5.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-25007 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25007 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_25007_validation.pdf.gz | 555.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_25007_full_validation.pdf.gz | 554.6 KB | 表示 | |
XML形式データ | emd_25007_validation.xml.gz | 14.1 KB | 表示 | |
CIF形式データ | emd_25007_validation.cif.gz | 19 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25007 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25007 | HTTPS FTP |
-関連構造データ
関連構造データ | 7sc0MC 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 | 類似検索 - 機能・相同性F&H 検索 |
-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_25007.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Refined and sharpened volume of the Caveolin-1 8S complex with applied C11 symmetry | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.98 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-試料の構成要素
-全体 : Caveolin-1 8S complex with C11 symmetry.
全体 | 名称: Caveolin-1 8S complex with C11 symmetry. |
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要素 |
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-超分子 #1: Caveolin-1 8S complex with C11 symmetry.
超分子 | 名称: Caveolin-1 8S complex with C11 symmetry. / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: Caveolin-1
分子 | 名称: Caveolin-1 / タイプ: protein_or_peptide / ID: 1 / コピー数: 11 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 20.494576 KDa |
組換発現 | 生物種: Escherichia coli BL21 (大腸菌) |
配列 | 文字列: MSGGKYVDSE GHLYTVPIRE QGNIYKPNNK AMADELSEKQ VYDAHTKEID LVNRDPKHLN DDVVKIDFED VIAEPEGTHS FDGIWKASF TTFTVTKYWF YRLLSALFGI PMALIWGIYF AILSFLHIWA VVPCIKSFLI EIQCISRVYS IYVHTVCDPL F EAVGKIFS NVRINLQKEI UniProtKB: Caveolin-1 |
-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 | 1.1 mg/mL | |||||||||||||||
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緩衝液 | pH: 8 構成要素:
詳細: Solutions were made fresh for each preparation of 8S particles | |||||||||||||||
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / メッシュ: 400 / 支持フィルム - 材質: GOLD / 支持フィルム - トポロジー: HOLEY ARRAY / 支持フィルム - Film thickness: 12 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. / 前処理 - 雰囲気: AIR / 詳細: 5 mA 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: 293 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | TFS GLACIOS |
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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: COUNTING / デジタル化 - サイズ - 横: 3838 pixel / デジタル化 - サイズ - 縦: 3710 pixel / デジタル化 - 画像ごとのフレーム数: 1-30 / 撮影したグリッド数: 1 / 実像数: 984 / 平均露光時間: 6.0 sec. / 平均電子線量: 55.5 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 100.0 µm / 最大 デフォーカス(補正後): 2.2 µm / 最小 デフォーカス(補正後): 1.5 µm / 倍率(補正後): 40103 / 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): 36000 |
試料ステージ | 試料ホルダーモデル: OTHER / ホルダー冷却材: NITROGEN |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: AB INITIO MODEL / 温度因子: 37.8 / 当てはまり具合の基準: Correlation coefficient |
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得られたモデル | PDB-7sc0: |