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データを開く
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基本情報
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タイトル | Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4 | ||||||||||||
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![]() | Ribosome / Membrane protein / Translocon / Transport | ||||||||||||
機能・相同性 | ![]() L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / muscle organ morphogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking ...L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / muscle organ morphogenesis / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / endoplasmic reticulum Sec complex / pronephric nephron development / positive regulation of growth hormone secretion / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane / positive regulation of organ growth / signal sequence binding / post-translational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane, translocation / insulin secretion / 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 / cytoplasmic microtubule / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein transmembrane transporter activity / protein-RNA complex assembly / cellular response to actinomycin D / rough endoplasmic reticulum / endoplasmic reticulum unfolded protein response / 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 / skeletal system development / positive regulation of translation / positive regulation of insulin secretion / cellular response to gamma radiation / phospholipid binding / mRNA 5'-UTR binding / transcription coactivator binding / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose metabolic process / ribosome binding / retina development in camera-type eye / regulation of translation / heparin binding / 5S rRNA binding / large ribosomal subunit rRNA binding / 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 / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / synapse / ubiquitin protein ligase 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 / cytoplasm 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.69243 Å | ||||||||||||
![]() | Lewis AJO / Hegde RS | ||||||||||||
資金援助 | ![]() ![]()
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![]() | ジャーナル: Biochem J / 年: 2021 タイトル: New tools for automated cryo-EM single-particle analysis in RELION-4.0. 著者: Dari Kimanius / Liyi Dong / Grigory Sharov / Takanori Nakane / Sjors H W Scheres / ![]() 要旨: We describe new tools for the processing of electron cryo-microscopy (cryo-EM) images in the fourth major release of the RELION software. In particular, we introduce VDAM, a variable-metric gradient ...We describe new tools for the processing of electron cryo-microscopy (cryo-EM) images in the fourth major release of the RELION software. In particular, we introduce VDAM, a variable-metric gradient descent algorithm with adaptive moments estimation, for image refinement; a convolutional neural network for unsupervised selection of 2D classes; and a flexible framework for the design and execution of multiple jobs in pre-defined workflows. In addition, we present a stand-alone utility called MDCatch that links the execution of jobs within this framework with metadata gathering during microscope data acquisition. The new tools are aimed at providing fast and robust procedures for unsupervised cryo-EM structure determination, with potential applications for on-the-fly processing and the development of flexible, high-throughput structure determination pipelines. We illustrate their potential on 12 publicly available cryo-EM data sets. | ||||||||||||
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構造の表示
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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 | ![]() | 263.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 72.7 KB 72.7 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 14.7 KB | 表示 | ![]() |
画像 | ![]() | 141.5 KB | ||
Filedesc metadata | ![]() | 15.6 KB | ||
その他 | ![]() ![]() | 224.8 MB 224.8 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 945.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 945.5 KB | 表示 | |
XML形式データ | ![]() | 22.4 KB | 表示 | |
CIF形式データ | ![]() | 29.9 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 | ![]() 8rjbMC 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 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.3398 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
-ハーフマップ: #1
ファイル | emd_19195_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_19195_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : 80S ribosome translating a stalled, two-TMD nascent chain (derive...
+超分子 #1: 80S ribosome translating a stalled, two-TMD nascent chain (derive...
+分子 #1: Protein transport protein Sec61 subunit alpha isoform 1
+分子 #2: Protein transport protein Sec61 subunit beta
+分子 #3: Protein transport protein Sec61 subunit gamma
+分子 #4: Stress-associated endoplasmic reticulum protein
+分子 #5: Ribosomal protein L8
+分子 #6: Nascent chain
+分子 #7: Large ribosomal subunit protein uL4
+分子 #8: Ribosomal_L18_c domain-containing protein
+分子 #9: 60S ribosomal protein L6
+分子 #10: Ribosomal Protein uL30
+分子 #11: 60S ribosomal protein L7a
+分子 #12: 60S ribosomal protein L9
+分子 #13: 60S ribosomal protein L10
+分子 #14: 60S ribosomal protein L11
+分子 #16: 60S ribosomal protein L13
+分子 #17: 60S ribosomal protein L14
+分子 #18: Ribosomal protein L15
+分子 #19: 60S ribosomal protein L13
+分子 #20: uL22
+分子 #21: Ribosomal protein L26
+分子 #22: Ribosomal protein L19
+分子 #23: 60S ribosomal protein L18a
+分子 #24: 60S ribosomal protein L21
+分子 #25: Ribosomal protein L22
+分子 #26: Ribosomal protein L23
+分子 #27: Ribosomal protein L24
+分子 #28: Ribosomal_L23eN domain-containing protein
+分子 #29: Ribosomal protein L26
+分子 #30: 60S ribosomal protein L27
+分子 #31: 60S ribosomal protein L27a
+分子 #32: 60S ribosomal protein L29
+分子 #33: Large ribosomal subunit protein eL30
+分子 #34: 60S ribosomal protein L31
+分子 #35: Ribosomal protein L32
+分子 #36: 60S ribosomal protein L35a
+分子 #37: 60S ribosomal protein L34
+分子 #38: 60S ribosomal protein L35
+分子 #39: 60S ribosomal protein L36
+分子 #40: Ribosomal protein L37
+分子 #41: 60S ribosomal protein L38
+分子 #42: 60S ribosomal protein L39-like
+分子 #43: eL40
+分子 #44: 60S ribosomal protein L41
+分子 #45: 60S ribosomal protein L36a-like
+分子 #46: 60S ribosomal protein L37a
+分子 #48: 60S ribosomal protein L28
+分子 #51: Ribosomal protein L3
+分子 #15: 28S rRNA
+分子 #47: P-site tRNA
+分子 #49: 5S rRNA
+分子 #50: 5.8S rRNA
+分子 #52: MAGNESIUM ION
+分子 #53: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.5 構成要素:
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 支持フィルム - 材質: GRAPHENE OXIDE / 支持フィルム - トポロジー: CONTINUOUS | ||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
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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: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 17540 / 平均電子線量: 54.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.7 µm 最小 デフォーカス(公称値): 1.9000000000000001 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
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得られたモデル | ![]() PDB-8rjb: |