+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-31496 | |||||||||
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タイトル | Structure of connexin43/Cx43/GJA1 gap junction intercellular channel in nanodiscs with soybean lipids at pH ~8.0 | |||||||||
マップデータ | Sharpened map of human Cx43/GJA1 connexin gap junction channel in nanodiscs | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 gap junction channel activity involved in cardiac conduction electrical coupling / negative regulation of gonadotropin secretion / positive regulation of striated muscle tissue development / milk ejection reflex / positive regulation of morphogenesis of an epithelium / positive regulation of mesodermal cell differentiation / atrial ventricular junction remodeling / cell communication by chemical coupling / cell communication by electrical coupling / columnar/cuboidal epithelial cell maturation ...gap junction channel activity involved in cardiac conduction electrical coupling / negative regulation of gonadotropin secretion / positive regulation of striated muscle tissue development / milk ejection reflex / positive regulation of morphogenesis of an epithelium / positive regulation of mesodermal cell differentiation / atrial ventricular junction remodeling / cell communication by chemical coupling / cell communication by electrical coupling / columnar/cuboidal epithelial cell maturation / glutathione transmembrane transporter activity / neuroblast migration / gap junction hemi-channel activity / negative regulation of trophoblast cell migration / monoatomic ion transmembrane transporter activity / microtubule-based transport / regulation of bone remodeling / regulation of ventricular cardiac muscle cell membrane depolarization / SARS-CoV-2 targets PDZ proteins in cell-cell junction / gap junction channel activity involved in cell communication by electrical coupling / contractile muscle fiber / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / gap junction assembly / atrial cardiac muscle cell action potential / cellular response to pH / Regulation of gap junction activity / skeletal muscle tissue regeneration / cardiac conduction system development / regulation of atrial cardiac muscle cell membrane depolarization / connexin complex / Golgi-associated vesicle membrane / Formation of annular gap junctions / fascia adherens / Gap junction degradation / export across plasma membrane / cell communication by electrical coupling involved in cardiac conduction / cell-cell contact zone / gap junction / bone remodeling / Gap junction assembly / gap junction channel activity / adult heart development / regulation of bone mineralization / regulation of ventricular cardiac muscle cell membrane repolarization / glutamate secretion / tight junction / blood vessel morphogenesis / lens development in camera-type eye / xenobiotic transport / intermediate filament / embryonic digit morphogenesis / maintenance of blood-brain barrier / efflux transmembrane transporter activity / heart looping / positive regulation of stem cell proliferation / RHOJ GTPase cycle / beta-tubulin binding / RHOQ GTPase cycle / establishment of mitotic spindle orientation / intercalated disc / lateral plasma membrane / alpha-tubulin binding / T cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / bone development / protein tyrosine kinase binding / tubulin binding / neuron migration / negative regulation of cell growth / beta-catenin binding / osteoblast differentiation / male gonad development / cellular response to amyloid-beta / positive regulation of cold-induced thermogenesis / protein localization / cell junction / cell-cell signaling / monoatomic ion transmembrane transport / heart development / scaffold protein binding / spermatogenesis / positive regulation of canonical NF-kappaB signal transduction / in utero embryonic development / apical plasma membrane / membrane raft / Golgi membrane / intracellular membrane-bounded organelle / negative regulation of gene expression / signaling receptor binding / focal adhesion / endoplasmic reticulum membrane / positive regulation of gene expression / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / nucleus / plasma membrane 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: 3.6 Å | |||||||||
データ登録者 | Lee HJ / Cha HJ / Jeong H / Lee SN / Lee CW / Woo JS | |||||||||
資金援助 | 韓国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Conformational changes in the human Cx43/GJA1 gap junction channel visualized using cryo-EM. 著者: Hyuk-Joon Lee / Hyung Jin Cha / Hyeongseop Jeong / Seu-Na Lee / Chang-Won Lee / Minsoo Kim / Jejoong Yoo / Jae-Sung Woo / 要旨: Connexin family proteins assemble into hexameric hemichannels in the cell membrane. The hemichannels dock together between two adjacent membranes to form gap junction intercellular channels (GJIChs). ...Connexin family proteins assemble into hexameric hemichannels in the cell membrane. The hemichannels dock together between two adjacent membranes to form gap junction intercellular channels (GJIChs). We report the cryo-electron microscopy structures of Cx43 GJICh, revealing the dynamic equilibrium state of various channel conformations in detergents and lipid nanodiscs. We identify three different N-terminal helix conformations of Cx43-gate-covering (GCN), pore-lining (PLN), and flexible intermediate (FIN)-that are randomly distributed in purified GJICh particles. The conformational equilibrium shifts to GCN by cholesteryl hemisuccinates and to PLN by C-terminal truncations and at varying pH. While GJIChs that mainly comprise GCN protomers are occluded by lipids, those containing conformationally heterogeneous protomers show markedly different pore sizes. We observe an α-to-π-helix transition in the first transmembrane helix, which creates a side opening to the membrane in the FIN and PLN conformations. This study provides basic structural information to understand the mechanisms of action and regulation of Cx43 GJICh. | |||||||||
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_31496.map.gz | 482.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-31496-v30.xml emd-31496.xml | 10.1 KB 10.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_31496.png | 40 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-31496 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31496 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_31496_validation.pdf.gz | 559.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_31496_full_validation.pdf.gz | 558.8 KB | 表示 | |
XML形式データ | emd_31496_validation.xml.gz | 8.1 KB | 表示 | |
CIF形式データ | emd_31496_validation.cif.gz | 9.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31496 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31496 | HTTPS FTP |
-関連構造データ
関連構造データ | 7f93MC 7f92C 7f94C 7xq9C 7xqbC 7xqdC 7xqfC 7xqgC 7xqhC 7xqiC 7xqjC 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_31496.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened map of human Cx43/GJA1 connexin gap junction channel in nanodiscs | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.5235 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 : Dodecameric complex of human Cx43/GJA1 in lipid nanodiscs (Soybea...
全体 | 名称: Dodecameric complex of human Cx43/GJA1 in lipid nanodiscs (Soybean polar extract) |
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要素 |
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-超分子 #1: Dodecameric complex of human Cx43/GJA1 in lipid nanodiscs (Soybea...
超分子 | 名称: Dodecameric complex of human Cx43/GJA1 in lipid nanodiscs (Soybean polar extract) タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1 詳細: Human Cx43 gap junction channel with gate-covering NTH conformation |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: Gap junction alpha-1 protein
分子 | 名称: Gap junction alpha-1 protein / タイプ: protein_or_peptide / ID: 1 / コピー数: 12 / 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: 43.061336 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG CENVCYDKSF PISHVRFWVL QIIFVSVPT LLYLAHVFYV MRKEEKLNKK EEELKVAQTD GVNVDMHLKQ IEIKKFKYGI EEHGKVKMRG GLLRTYIISI L FKSIFEVA ...文字列: MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG CENVCYDKSF PISHVRFWVL QIIFVSVPT LLYLAHVFYV MRKEEKLNKK EEELKVAQTD GVNVDMHLKQ IEIKKFKYGI EEHGKVKMRG GLLRTYIISI L FKSIFEVA FLLIQWYIYG FSLSAVYTCK RDPCPHQVDC FLSRPTEKTI FIIFMLVVSL VSLALNIIEL FYVFFKGVKD RV KGKSDPY HATSGALSPA KDCGSQKYAY FNGCSSPTAP LSPMSPPGYK LVTGDRNNSS CRNYNKQASE QNWANYSAEQ NRM GQAGST ISNSHAQPFD FPDDNQNSKK LAAGHELQPL AIVDQRPSSR ASSRASSRPR PDDLEI |
-分子 #2: TETRADECANE
分子 | 名称: TETRADECANE / タイプ: ligand / ID: 2 / コピー数: 120 / 式: C14 |
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分子量 | 理論値: 198.388 Da |
Chemical component information | ChemComp-C14: |
-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
緩衝液 | pH: 8 |
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凍結 | 凍結剤: ETHANE |
-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: FEI FALCON III (4k x 4k) 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: EMDB MAP EMDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 28341 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |