+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3jc2 | ||||||
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タイトル | The structure of the mammalian Sec61 channel opened by a signal sequence | ||||||
要素 |
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キーワード | TRANSPORT PROTEIN / Sec61 / translocation / signal sequence | ||||||
機能・相同性 | 機能・相同性情報 : / Growth hormone receptor signaling / long-day photoperiodism / response to external biotic stimulus / negative regulation of nitric oxide mediated signal transduction / peptide hormone secretion / prolactin receptor binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / positive regulation of lactation ...: / Growth hormone receptor signaling / long-day photoperiodism / response to external biotic stimulus / negative regulation of nitric oxide mediated signal transduction / peptide hormone secretion / prolactin receptor binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / positive regulation of lactation / regulation of meiotic cell cycle process involved in oocyte maturation / pronephric nephron development / response to L-arginine / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein insertion into ER membrane / positive regulation of fatty acid biosynthetic process / mammary gland development / signal transduction involved in regulation of gene expression / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / post-translational protein targeting to membrane, translocation / blastocyst formation / response to food / biosynthetic process / positive regulation of endocytosis / protein transmembrane transporter activity / response to mechanical stimulus / lactation / response to nutrient levels / female pregnancy / positive regulation of receptor signaling pathway via JAK-STAT / hormone activity / phospholipid binding / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of nitric oxide biosynthetic process / ribosome binding / positive regulation of NF-kappaB transcription factor activity / endoplasmic reticulum lumen / negative regulation of gene expression / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / extracellular region / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Bos taurus (ウシ) Canis lupus familiaris (イヌ) | ||||||
手法 | 電子顕微鏡法 / 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 | Voorhees, R.M. / Hegde, R.S. | ||||||
引用 | ジャーナル: Science / 年: 2016 タイトル: Structure of the Sec61 channel opened by a signal sequence. 著者: Rebecca M Voorhees / Ramanujan S Hegde / 要旨: Secreted and integral membrane proteins compose up to one-third of the biological proteome. These proteins contain hydrophobic signals that direct their translocation across or insertion into the ...Secreted and integral membrane proteins compose up to one-third of the biological proteome. These proteins contain hydrophobic signals that direct their translocation across or insertion into the lipid bilayer by the Sec61 protein-conducting channel. The molecular basis of how hydrophobic signals within a nascent polypeptide trigger channel opening is not understood. Here, we used cryo-electron microscopy to determine the structure of an active Sec61 channel that has been opened by a signal sequence. The signal supplants helix 2 of Sec61α, which triggers a rotation that opens the central pore both axially across the membrane and laterally toward the lipid bilayer. Comparisons with structures of Sec61 in other states suggest a pathway for how hydrophobic signals engage the channel to gain access to the lipid bilayer. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 3jc2.cif.gz | 106.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3jc2.ent.gz | 85.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3jc2.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/jc/3jc2 ftp://data.pdbj.org/pub/pdb/validation_reports/jc/3jc2 | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 52279.379 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: purified from native canine microsomes / 由来: (天然) Canis lupus familiaris (イヌ) / 参照: UniProt: P38377 |
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#2: タンパク質 | 分子量: 7019.456 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: purified from native canine microsomes / 由来: (天然) Canis lupus familiaris (イヌ) / 参照: UniProt: P60058 |
#3: タンパク質・ペプチド | 分子量: 2053.576 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bos taurus (ウシ) / 遺伝子: prolactin / 発現宿主: Oryctolagus cuniculus (ウサギ) Tissue fraction (発現宿主): reticulocyte translation extract in the presence of canine microsomes 参照: UniProt: Q6VMP1, UniProt: P01239*PLUS |
#4: タンパク質・ペプチド | 分子量: 2741.370 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: purified from native canine microsomes / 由来: (天然) Canis lupus familiaris (イヌ) |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 |
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緩衝液 | 名称: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin pH: 7.5 詳細: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin | ||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
試料支持 | 詳細: Quantifoil (R2/2) holey carbon grid covered in a 70 Angstrom-thick layer of amorphous carbon | ||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK I / 凍結剤: ETHANE / 湿度: 100 % 詳細: 3 uL sample was added to the grid, incubated for 30 seconds at 4 C, blotted for 9 seconds, and then plunged into liquid ethane (FEI VITROBOT). 手法: 3 uL sample was added to the grid, incubated for 30 seconds at 4 C, blotted for 9 seconds |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS / 日付: 2015年3月6日 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 59000 X / 倍率(補正後): 104478 X / 最大 デフォーカス(公称値): 3500 nm / 最小 デフォーカス(公称値): 2000 nm |
撮影 | 電子線照射量: 27 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
-解析
EMソフトウェア |
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対称性 | 点対称性: C1 (非対称) | |||||||||||||||
3次元再構成 | 解像度: 3.6 Å / 粒子像の数: 101339 / ピクセルサイズ(公称値): 1.34 Å / ピクセルサイズ(実測値): 1.34 Å / 対称性のタイプ: POINT | |||||||||||||||
原子モデル構築 | 空間: REAL / Target criteria: R-factor 詳細: DETAILS--Real-space fitting using Chimera and Coot followed by reciprocal-space refinement using REFMAC | |||||||||||||||
原子モデル構築 |
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精密化ステップ | サイクル: LAST
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