+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-30432 | ||||||||||||
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タイトル | Cryo-EM structure of 80S ribosome from mouse kidney | ||||||||||||
マップデータ | ribosome from mouse kidney | ||||||||||||
試料 |
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キーワード | 80S mouse ribosome / protein translation / RPL39 / RPL39L / kidney ribosome / RIBOSOME | ||||||||||||
機能・相同性 | 機能・相同性情報 TNFR1-mediated ceramide production / 5.8S rRNA binding / Protein hydroxylation / translation at postsynapse / Formation of the ternary complex, and subsequently, the 43S complex / positive regulation of amide metabolic process / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) ...TNFR1-mediated ceramide production / 5.8S rRNA binding / Protein hydroxylation / translation at postsynapse / Formation of the ternary complex, and subsequently, the 43S complex / positive regulation of amide metabolic process / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Downregulation of ERBB2:ERBB3 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / IRAK2 mediated activation of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of expression of SLITs and ROBOs / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Alpha-protein kinase 1 signaling pathway / Stabilization of p53 / Formation of a pool of free 40S subunits / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / Regulation of NF-kappa B signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / SRP-dependent cotranslational protein targeting to membrane / Regulation of BACH1 activity / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Major pathway of rRNA processing in the nucleolus and cytosol / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Regulation of innate immune responses to cytosolic DNA / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Protein methylation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / PINK1-PRKN Mediated Mitophagy / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / Termination of translesion DNA synthesis / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Inactivation of CSF3 (G-CSF) signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Senescence-Associated Secretory Phenotype (SASP) / TNFR1-induced NF-kappa-B signaling pathway / Josephin domain DUBs / Dual Incision in GG-NER / Downregulation of ERBB2 signaling / Regulation of FZD by ubiquitination / Dual incision in TC-NER / IKK complex recruitment mediated by RIP1 / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Oncogene Induced Senescence / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Ubiquitin-dependent degradation of Cyclin D / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Metalloprotease DUBs / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TNFR1 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of necroptotic cell death / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Degradation of AXIN 類似検索 - 分子機能 | ||||||||||||
生物種 | Mus musculus (ハツカネズミ) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.82 Å | ||||||||||||
データ登録者 | Huo YG / He X | ||||||||||||
資金援助 | 中国, 3件
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引用 | ジャーナル: Nature / 年: 2022 タイトル: A male germ-cell-specific ribosome controls male fertility. 著者: Huiling Li / Yangao Huo / Xi He / Liping Yao / Hao Zhang / Yiqiang Cui / Huijuan Xiao / Wenxiu Xie / Dejiu Zhang / Yue Wang / Shu Zhang / Haixia Tu / Yiwei Cheng / Yueshuai Guo / Xintao Cao / ...著者: Huiling Li / Yangao Huo / Xi He / Liping Yao / Hao Zhang / Yiqiang Cui / Huijuan Xiao / Wenxiu Xie / Dejiu Zhang / Yue Wang / Shu Zhang / Haixia Tu / Yiwei Cheng / Yueshuai Guo / Xintao Cao / Yunfei Zhu / Tao Jiang / Xuejiang Guo / Yan Qin / Jiahao Sha / 要旨: Ribosomes are highly sophisticated translation machines that have been demonstrated to be heterogeneous in the regulation of protein synthesis. Male germ cell development involves complex ...Ribosomes are highly sophisticated translation machines that have been demonstrated to be heterogeneous in the regulation of protein synthesis. Male germ cell development involves complex translational regulation during sperm formation. However, it remains unclear whether translation during sperm formation is performed by a specific ribosome. Here we report a ribosome with a specialized nascent polypeptide exit tunnel, Ribosome, that is assembled with the male germ-cell-specific protein RPL39L, the paralogue of core ribosome (Ribosome) protein RPL39. Deletion of Ribosome in mice causes defective sperm formation, resulting in substantially reduced fertility. Our comparison of single-particle cryo-electron microscopy structures of ribosomes from mouse kidneys and testes indicates that Ribosome features a ribosomal polypeptide exit tunnel of distinct size and charge states compared with Ribosome. Ribosome predominantly cotranslationally regulates the folding of a subset of male germ-cell-specific proteins that are essential for the formation of sperm. Moreover, we found that specialized functions of Ribosome were not replaceable by Ribosome. Taken together, identification of this sperm-specific ribosome should greatly expand our understanding of ribosome function and tissue-specific regulation of protein expression pattern in mammals. | ||||||||||||
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_30432.map.gz | 229 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-30432-v30.xml emd-30432.xml | 96.4 KB 96.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_30432.png | 66 KB | ||
Filedesc metadata | emd-30432.cif.gz | 19.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-30432 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30432 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_30432_validation.pdf.gz | 687.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_30432_full_validation.pdf.gz | 687.1 KB | 表示 | |
XML形式データ | emd_30432_validation.xml.gz | 6.9 KB | 表示 | |
CIF形式データ | emd_30432_validation.cif.gz | 7.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30432 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30432 | 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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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_30432.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | ribosome from mouse kidney | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.04 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
-試料の構成要素
+全体 : Mus musculus 80S ribosome from kidney
+超分子 #1: Mus musculus 80S ribosome from kidney
+分子 #1: 60S ribosomal protein L8
+分子 #2: 40S ribosomal protein SA
+分子 #3: 60S ribosomal protein L3
+分子 #4: 40S ribosomal protein S3a
+分子 #5: 60S ribosomal protein L4
+分子 #6: 60S ribosomal protein L5
+分子 #7: 60S ribosomal protein L6
+分子 #8: 60S ribosomal protein L7
+分子 #9: 60S ribosomal protein L7a
+分子 #10: 60S ribosomal protein L9
+分子 #11: 60S ribosomal protein L10
+分子 #12: 60S ribosomal protein L11
+分子 #13: 60S ribosomal protein L13
+分子 #14: 60S ribosomal protein L14
+分子 #15: 60S ribosomal protein L15
+分子 #16: 60S ribosomal protein L13a
+分子 #17: 60S ribosomal protein L17
+分子 #18: 60S ribosomal protein L18
+分子 #19: 60S ribosomal protein L19
+分子 #20: 60S ribosomal protein L18a
+分子 #21: 60S ribosomal protein L21
+分子 #22: 60S ribosomal protein L22
+分子 #23: 60S ribosomal protein L23
+分子 #24: 60S ribosomal protein L24
+分子 #25: 60S ribosomal protein L23a
+分子 #26: 60S ribosomal protein L26
+分子 #27: 60S ribosomal protein L27
+分子 #28: 60S ribosomal protein L27a
+分子 #29: 60S ribosomal protein L29
+分子 #30: 60S ribosomal protein L30
+分子 #31: 60S ribosomal protein L31
+分子 #32: 60S ribosomal protein L32
+分子 #33: 60S ribosomal protein L35a
+分子 #34: 60S ribosomal protein L34
+分子 #35: 60S ribosomal protein L35
+分子 #36: 60S ribosomal protein L36
+分子 #37: 60S ribosomal protein L37
+分子 #38: 60S ribosomal protein L38
+分子 #39: Ubiquitin-60S ribosomal protein L40
+分子 #40: 60S ribosomal protein L41
+分子 #41: 60S ribosomal protein L36a
+分子 #42: 60S ribosomal protein L37a
+分子 #43: 60S ribosomal protein L28
+分子 #48: 40S ribosomal protein S3
+分子 #49: 40S ribosomal protein S4, X isoform
+分子 #50: 40S ribosomal protein S5
+分子 #51: 40S ribosomal protein S7
+分子 #52: 40S ribosomal protein S8
+分子 #53: 40S ribosomal protein S10
+分子 #54: 40S ribosomal protein S11
+分子 #55: 40S ribosomal protein S15
+分子 #56: 40S ribosomal protein S16
+分子 #57: 40S ribosomal protein S17
+分子 #58: 40S ribosomal protein S18
+分子 #59: 40S ribosomal protein S19
+分子 #60: 40S ribosomal protein S20
+分子 #61: 40S ribosomal protein S21
+分子 #62: 40S ribosomal protein S23
+分子 #63: 40S ribosomal protein S26
+分子 #64: 40S ribosomal protein S28
+分子 #65: 40S ribosomal protein S29
+分子 #66: Receptor of activated protein C kinase 1
+分子 #67: 40S ribosomal protein S2
+分子 #68: 40S ribosomal protein S6
+分子 #69: 40S ribosomal protein S9
+分子 #70: 40S ribosomal protein S13
+分子 #71: 40S ribosomal protein S14
+分子 #72: 40S ribosomal protein S15a
+分子 #73: 40S ribosomal protein S24
+分子 #74: 40S ribosomal protein S25
+分子 #75: 40S ribosomal protein S27
+分子 #76: 40S ribosomal protein S30
+分子 #78: Ribosomal protein L39
+分子 #44: Mus musculus 28S ribosomal RNA
+分子 #45: Mus musculus 5S ribosomal RNA
+分子 #46: Mus musculus 5.8S ribosomal RNA
+分子 #47: Mus musculus 18S ribosomal RNA
+分子 #77: tRNA
+分子 #79: MAGNESIUM ION
+分子 #80: ZINC ION
+分子 #81: water
-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
緩衝液 | pH: 7.5 構成要素:
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グリッド | モデル: Quantifoil / 材質: GOLD / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY | |||||||||||||||
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 |
-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 K2 SUMMIT (4k x 4k) 平均電子線量: 60.0 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 1.5 µm / 最小 デフォーカス(公称値): 1.0 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.82 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 280287 |
初期 角度割当 | タイプ: ANGULAR RECONSTITUTION |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION |