+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 7ado | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of human ER membrane protein complex in lipid nanodiscs | |||||||||
![]() |
| |||||||||
![]() | MEMBRANE PROTEIN / ER membrane protein / EMC / Membrane protein biogenesis | |||||||||
機能・相同性 | ![]() extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / Miscellaneous transport and binding events / tail-anchored membrane protein insertion into ER membrane / magnesium ion transmembrane transporter activity ...extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / Miscellaneous transport and binding events / tail-anchored membrane protein insertion into ER membrane / magnesium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / protein folding in endoplasmic reticulum / copper ion transport / autophagosome assembly / RHOA GTPase cycle / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / positive regulation of angiogenesis / early endosome membrane / carbohydrate binding / angiogenesis / early endosome / Golgi membrane / apoptotic process / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / protein-containing complex / extracellular region / membrane / 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: 3.39 Å | |||||||||
![]() | Braeuning, B. / Prabu, J.R. / Miller-Vedam, L.E. / Weissman, J.S. / Frost, A. / Schulman, B.A. | |||||||||
資金援助 | ![]()
| |||||||||
![]() | ![]() タイトル: Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. 著者: Lakshmi E Miller-Vedam / Bastian Bräuning / Katerina D Popova / Nicole T Schirle Oakdale / Jessica L Bonnar / Jesuraj R Prabu / Elizabeth A Boydston / Natalia Sevillano / Matthew J Shurtleff ...著者: Lakshmi E Miller-Vedam / Bastian Bräuning / Katerina D Popova / Nicole T Schirle Oakdale / Jessica L Bonnar / Jesuraj R Prabu / Elizabeth A Boydston / Natalia Sevillano / Matthew J Shurtleff / Robert M Stroud / Charles S Craik / Brenda A Schulman / Adam Frost / Jonathan S Weissman / ![]() ![]() 要旨: Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player ...Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies distinguish between two separable EMC activities, as an insertase regulating tail-anchored protein levels and a broader role in polytopic membrane protein biogenesis. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC's multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes. | |||||||||
履歴 |
|
-
構造の表示
ムービー |
![]() |
---|---|
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 | ![]() | 390.3 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 318.1 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.5 MB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 1.5 MB | 表示 | |
XML形式データ | ![]() | 76.1 KB | 表示 | |
CIF形式データ | ![]() | 111.7 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
-
集合体
登録構造単位 | ![]()
|
---|---|
1 |
|
-
要素
-ER membrane protein complex subunit ... , 8種, 8分子 ABCDFGHI
#1: タンパク質 | 分子量: 111886.141 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
---|---|
#2: タンパク質 | 分子量: 34882.531 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
#3: タンパク質 | 分子量: 29981.924 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
#4: タンパク質 | 分子量: 20104.572 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: There is no mutations but sequence from model and input are not aligning well. 由来: (組換発現) ![]() ![]() |
#6: タンパク質 | 分子量: 12029.248 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
#7: タンパク質 | 分子量: 26501.586 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
#8: タンパク質 | 分子量: 23807.076 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: Map modelled as EMC8; both EMC8 and its paralog EMC9 (44% identity) were co-expressed and turns out they can both occupy same position on complex in mutually exclusive manner. We chose to ...詳細: Map modelled as EMC8; both EMC8 and its paralog EMC9 (44% identity) were co-expressed and turns out they can both occupy same position on complex in mutually exclusive manner. We chose to model as EMC8 but note that map is likely superposition of both. 由来: (組換発現) ![]() 遺伝子: EMC8, C16orf2, C16orf4, COX4AL, COX4NB, FAM158B, NOC4 プラスミド: pEG / 細胞株 (発現宿主): HEK293 GnTI- / 発現宿主: ![]() |
#9: タンパク質 | 分子量: 27446.875 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
-タンパク質 / タンパク質・ペプチド / 糖 / 非ポリマー , 4種, 11分子 EK![](data/chem/img/NAG.gif)
![](data/chem/img/PCW.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/PCW.gif)
#10: タンパク質・ペプチド | 分子量: 1379.692 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: This is transmembrane alpha-helix which was modeled as poly-alanine. 由来: (組換発現) ![]() ![]() | ||||
---|---|---|---|---|---|
#11: 糖 | ChemComp-NAG / #12: 化合物 | ChemComp-PCW / #5: タンパク質 | | 分子量: 15703.762 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
-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: Human endoplasmic reticulum membrane protein complex (EMC) in POPC nanodiscs タイプ: COMPLEX / Entity ID: #1-#10 / 由来: RECOMBINANT |
---|---|
分子量 | 値: 0.3 MDa |
由来(天然) | 生物種: ![]() |
由来(組換発現) | 生物種: ![]() |
緩衝液 | pH: 6 詳細: 10 mM ammonium citrate pH 6.0, 100 mM sodium chloride, 0.25 mM TCEP |
試料 | 濃度: 2 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 |
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
-
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 / 日付: 2019年12月23日 |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 平均露光時間: 3 sec. / 電子線照射量: 72 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-
解析
EMソフトウェア |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||
3次元再構成 | 解像度: 3.39 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 177560 / 対称性のタイプ: POINT | |||||||||||||||
原子モデル構築 | プロトコル: AB INITIO MODEL |