+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 7tut | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in complex with the multipass translocon | ||||||||||||
![]() |
| ||||||||||||
![]() | RIBOSOME / Membrane protein / translocon | ||||||||||||
機能・相同性 | ![]() multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / endoplasmic reticulum Sec complex / protein localization to nuclear inner membrane / pronephric nephron development / rough endoplasmic reticulum membrane / cotranslational protein targeting to membrane / Sec61 translocon complex / protein targeting to ER ...multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / endoplasmic reticulum Sec complex / protein localization to nuclear inner membrane / pronephric nephron development / rough endoplasmic reticulum membrane / cotranslational protein targeting to membrane / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane / signal sequence binding / endoplasmic reticulum calcium ion homeostasis / post-translational protein targeting to membrane, translocation / protein folding chaperone complex / SRP-dependent cotranslational protein targeting to membrane, translocation / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / G1 to G0 transition / ER overload response / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein transmembrane transporter activity / regulation of signal transduction / protein-RNA complex assembly / cellular response to actinomycin D / ERAD pathway / rough endoplasmic reticulum / protein folding chaperone / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-embryonic development / maturation of LSU-rRNA / ribosomal large subunit biogenesis / positive regulation of translation / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / modification-dependent protein catabolic process / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / protein tag activity / ribosome binding / retina development in camera-type eye / regulation of translation / heparin binding / 5S rRNA binding / large ribosomal subunit rRNA binding / nuclear membrane / defense response to Gram-negative bacterium / killing of cells of another organism / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / postsynaptic density / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / synapse / calcium ion binding / positive regulation of cell population proliferation / positive regulation of gene expression / endoplasmic reticulum membrane / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() ![]() ![]() ![]() | ||||||||||||
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: 3.88 Å | ||||||||||||
![]() | Kim, M.K. / Lewis, A.J.O. / Keenan, R.J. / Hegde, R.S. | ||||||||||||
資金援助 | ![]()
| ||||||||||||
![]() | ![]() タイトル: Mechanism of an intramembrane chaperone for multipass membrane proteins. 著者: Luka Smalinskaitė / Min Kyung Kim / Aaron J O Lewis / Robert J Keenan / Ramanujan S Hegde / ![]() ![]() 要旨: Multipass membrane proteins play numerous roles in biology and include receptors, transporters, ion channels and enzymes. How multipass proteins are co-translationally inserted and folded at the ...Multipass membrane proteins play numerous roles in biology and include receptors, transporters, ion channels and enzymes. How multipass proteins are co-translationally inserted and folded at the endoplasmic reticulum is not well understood. The prevailing model posits that each transmembrane domain (TMD) of a multipass protein successively passes into the lipid bilayer through a front-side lateral gate of the Sec61 protein translocation channel. The PAT complex, an intramembrane chaperone comprising Asterix and CCDC47, engages early TMDs of multipass proteins to promote their biogenesis by an unknown mechanism. Here, biochemical and structural analysis of intermediates during multipass protein biogenesis showed that the nascent chain is not engaged with Sec61, which is occluded and latched closed by CCDC47. Instead, Asterix binds to and redirects the substrate to a location behind Sec61, where the PAT complex contributes to a multipass translocon surrounding a semi-enclosed, lipid-filled cavity. Detection of multiple TMDs in this cavity after their emergence from the ribosome suggests that multipass proteins insert and fold behind Sec61. Accordingly, biogenesis of several multipass proteins was unimpeded by inhibitors of the Sec61 lateral gate. These findings elucidate the mechanism of an intramembrane chaperone and suggest a new framework for multipass membrane protein biogenesis at the endoplasmic reticulum. | ||||||||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 5.5 MB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 表示 | ![]() | |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.2 MB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 1.3 MB | 表示 | |
XML形式データ | ![]() | 232.1 KB | 表示 | |
CIF形式データ | ![]() | 413.9 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 26133MC ![]() 7tm3C C: 同じ文献を引用 ( M: このデータのモデリングに利用したマップデータ |
---|---|
類似構造データ | 類似検索 - 機能・相同性 ![]() |
-
リンク
-
集合体
登録構造単位 | ![]()
|
---|---|
1 |
|
-
要素
+タンパク質 , 49種, 49分子 ACDEFGHIJLMNOPQRSTUVWXYZabcdef...
-タンパク質・ペプチド , 1種, 1分子 n
#38: タンパク質・ペプチド | 分子量: 3473.451 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
---|
-RNA鎖 , 4種, 4分子 quvK
#41: RNA鎖 | 分子量: 24632.648 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
---|---|
#43: RNA鎖 | 分子量: 38691.914 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
#44: RNA鎖 | 分子量: 50143.648 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
#55: RNA鎖 | 分子量: 1148115.375 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
-Protein transport protein Sec61 subunit ... , 2種, 2分子 12
#47: タンパク質 | 分子量: 52279.379 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
---|---|
#48: タンパク質 | 分子量: 9987.456 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() ![]() |
-非ポリマー , 2種, 225分子 ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#57: 化合物 | ChemComp-MG / #58: 化合物 | ChemComp-ZN / |
---|
-詳細
研究の焦点であるリガンドがあるか | N |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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 | 名称: 80S ribosome translating a stalled, four-TMD nascent chain (derived from rhodopsin), and bound to components of the multi-pass translocon タイプ: RIBOSOME / 詳細: Sample prepared by in vitro translation / Entity ID: #1-#56 / 由来: MULTIPLE SOURCES |
---|---|
分子量 | 実験値: NO |
緩衝液 | pH: 7.5 詳細: 50 mM HEPES-KOH, pH 7.5, 200 mM potassium acetate, 5 mM magnesium acetate, 0.25% digitonin, 50 mM biotin |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K 詳細: Blot for 4 seconds with Whatman filter papers at a blot force of -15 before plunging. |
-
電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2700 nm / 最小 デフォーカス(公称値): 1900 nm |
撮影 | 電子線照射量: 54 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 13755 |
-
解析
ソフトウェア |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EMソフトウェア |
| ||||||||||||||||||||||||
CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.88 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 136812 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL | ||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 276.11 Å2 | ||||||||||||||||||||||||
拘束条件 |
|