+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-20914 | |||||||||
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タイトル | Human Connexin-26 (Neutral pH open conformation) | |||||||||
マップデータ | Sharpened map at 4.0 A resolution. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 Transport of connexons to the plasma membrane / response to human chorionic gonadotropin / gap junction-mediated intercellular transport / epididymis development / gap junction channel activity involved in cell communication by electrical coupling / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / gap junction ...Transport of connexons to the plasma membrane / response to human chorionic gonadotropin / gap junction-mediated intercellular transport / epididymis development / gap junction channel activity involved in cell communication by electrical coupling / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / gap junction / astrocyte projection / Gap junction assembly / gap junction channel activity / cellular response to glucagon stimulus / inner ear development / decidualization / endoplasmic reticulum-Golgi intermediate compartment / lateral plasma membrane / response to retinoic acid / cellular response to dexamethasone stimulus / response to ischemia / response to progesterone / sensory perception of sound / transmembrane transport / cell-cell signaling / response to estradiol / cellular response to oxidative stress / cell body / response to lipopolysaccharide / calcium ion binding / perinuclear region of cytoplasm / identical protein binding / 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: 4.0 Å | |||||||||
データ登録者 | Khan AK / Jagielnicki M / Purdy MD / Yeager M | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Cell Rep / 年: 2020 タイトル: A Steric "Ball-and-Chain" Mechanism for pH-Mediated Regulation of Gap Junction Channels. 著者: Ali K Khan / Maciej Jagielnicki / William E McIntire / Michael D Purdy / Venkatasubramanian Dharmarajan / Patrick R Griffin / Mark Yeager / 要旨: Gap junction channels (GJCs) mediate intercellular communication and are gated by numerous conditions such as pH. The electron cryomicroscopy (cryo-EM) structure of Cx26 GJC at physiological pH ...Gap junction channels (GJCs) mediate intercellular communication and are gated by numerous conditions such as pH. The electron cryomicroscopy (cryo-EM) structure of Cx26 GJC at physiological pH recapitulates previous GJC structures in lipid bilayers. At pH 6.4, we identify two conformational states, one resembling the open physiological-pH structure and a closed conformation that displays six threads of density, that join to form a pore-occluding density. Crosslinking and hydrogen-deuterium exchange mass spectrometry reveal closer association between the N-terminal (NT) domains and the cytoplasmic loops (CL) at acidic pH. Previous electrophysiologic studies suggest an association between NT residue N14 and H100 near M2, which may trigger the observed movement of M2 toward M1 in our cryo-EM maps, thereby accounting for additional NT-CL crosslinks at acidic pH. We propose that these pH-induced interactions and conformational changes result in extension, ordering, and association of the acetylated NT domains to form a hexameric "ball-and-chain" gating particle. | |||||||||
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_20914.map.gz | 56.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-20914-v30.xml emd-20914.xml | 16.1 KB 16.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_20914.png | 68.7 KB | ||
その他 | emd_20914_additional.map.gz | 45.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-20914 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20914 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_20914_validation.pdf.gz | 527.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_20914_full_validation.pdf.gz | 527.5 KB | 表示 | |
XML形式データ | emd_20914_validation.xml.gz | 6 KB | 表示 | |
CIF形式データ | emd_20914_validation.cif.gz | 6.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20914 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20914 | 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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-マップ
ファイル | ダウンロード / ファイル: emd_20914.map.gz / 形式: CCP4 / 大きさ: 61 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened map at 4.0 A resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 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
-追加マップ: Not sharpened map at 4.4 A resolution.
ファイル | emd_20914_additional.map | ||||||||||||
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注釈 | Not sharpened map at 4.4 A resolution. | ||||||||||||
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 : Connexin-26 Gap Junction Channel
全体 | 名称: Connexin-26 Gap Junction Channel |
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要素 |
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-超分子 #1: Connexin-26 Gap Junction Channel
超分子 | 名称: Connexin-26 Gap Junction Channel / タイプ: organelle_or_cellular_component / 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) |
分子量 | 理論値: 326 kDa/nm |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
-分子 #1: Gap junction beta-2 protein
分子 | 名称: Gap junction beta-2 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: 26.214945 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: MDWGTLQTIL GGVNKHSTSI GKIWLTVLFI FRIMILVVAA KEVWGDEQAD FVCNTLQPGC KNVCYDHYFP ISHIRLWALQ LIFVSTPAL LVAMHVAYRR HEKKRKFIKG EIKSEFKDIE EIKTQKVRIE GSLWWTYTSS IFFRVIFEAA FMYVFYVMYD G FSMQRLVK ...文字列: MDWGTLQTIL GGVNKHSTSI GKIWLTVLFI FRIMILVVAA KEVWGDEQAD FVCNTLQPGC KNVCYDHYFP ISHIRLWALQ LIFVSTPAL LVAMHVAYRR HEKKRKFIKG EIKSEFKDIE EIKTQKVRIE GSLWWTYTSS IFFRVIFEAA FMYVFYVMYD G FSMQRLVK CNAWPCPNTV DCFVSRPTEK TVFTVFMIAV SGICILLNVT ELSYLLIRYS SGKSKKPV |
-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 | 0.4 mg/mL | |||||||||
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緩衝液 | pH: 7.5 構成要素:
詳細: NaCl was diluted from 1 M to 200 mM immediately before freezing. | |||||||||
グリッド | モデル: C-flat-2/2 | |||||||||
凍結 | 凍結剤: ETHANE / 装置: HOMEMADE PLUNGER 詳細: After application of sample to the C-flat holey carbon grid, sample was manually blotted with Whatman no. 1 filter paper for 3-5 s.. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Quantum LS / エネルギーフィルター - スリット幅: 20 eV |
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 / 撮影したグリッド数: 1 / 平均露光時間: 8.0 sec. / 平均電子線量: 45.0 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: SPOT SCAN / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 倍率(公称値): 130000 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
詳細 | Initial local fitting was done using UCSF Chimera. Multiple rounds of automated (Phenix) and manual (Coot) model building were performed. The model was validated in Molprobity(part of Phenix package). Model-map cross correlation score as well as EMRinger score were obtained in Phenix. RMSD values for C-alphas were calculated in UCSF Chimera. |
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精密化 | 空間: REAL / プロトコル: OTHER / 当てはまり具合の基準: Model-map cross correlation |
得られたモデル | PDB-6uvr: |