+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23938 | |||||||||
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タイトル | Cryo-EM structure of the human SSU processome, state post-A1 | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 preribosome / nucleolar exosome (RNase complex) / oocyte growth / nucleologenesis / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / snoRNA localization / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / granular component ...preribosome / nucleolar exosome (RNase complex) / oocyte growth / nucleologenesis / 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / snoRNA localization / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / granular component / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / positive regulation of mRNA cis splicing, via spliceosome / regulation of telomerase RNA localization to Cajal body / TRAMP-dependent tRNA surveillance pathway / positive regulation of male gonad development / CUT catabolic process / RNA exonuclease activity / exosome (RNase complex) / U4atac snRNP / nuclear polyadenylation-dependent rRNA catabolic process / CURI complex / regulation of stem cell population maintenance / cytoplasmic exosome (RNase complex) / t-UTP complex / nuclear exosome (RNase complex) / UTP-C complex / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / U4atac snRNA binding / rRNA (pseudouridine) methyltransferase activity / poly(A)-dependent snoRNA 3'-end processing / histone H2AQ104 methyltransferase activity / pre-snoRNP complex / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / rRNA (adenine-N6,N6-)-dimethyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone mRNA catabolic process / dense fibrillar component / nuclear mRNA surveillance / box C/D sno(s)RNA 3'-end processing / tRNA export from nucleus / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / histone methyltransferase binding / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of transcription elongation by RNA polymerase II / positive regulation of rRNA processing / transcription elongation factor activity / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / rRNA primary transcript binding / cilium disassembly / : / blastocyst formation / rRNA base methylation / Cul4-RING E3 ubiquitin ligase complex / RNA splicing, via transesterification reactions / negative regulation of RNA splicing / sno(s)RNA-containing ribonucleoprotein complex / protein localization to nucleolus / response to stimulus / U4 snRNA binding / box C/D methylation guide snoRNP complex / SUMOylation of RNA binding proteins / U2-type precatalytic spliceosome / RNA catabolic process / telomerase RNA binding / neural crest cell differentiation / rRNA methylation / box C/D snoRNP assembly / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / U3 snoRNA binding / nuclear-transcribed mRNA catabolic process / Translation initiation complex formation / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / preribosome, small subunit precursor / mammalian oogenesis stage / snoRNA binding / activation-induced cell death of T cells / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / maturation of 5.8S rRNA / fibroblast growth factor binding / Protein hydroxylation / RNA polymerase II complex binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / monocyte chemotaxis 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Human (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.7 Å | |||||||||
データ登録者 | Vanden Broeck A / Singh S / Klinge S | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Science / 年: 2021 タイトル: Nucleolar maturation of the human small subunit processome. 著者: Sameer Singh / Arnaud Vanden Broeck / Linamarie Miller / Malik Chaker-Margot / Sebastian Klinge / 要旨: The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. We report the high-resolution ...The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. We report the high-resolution cryo–electron microscopy structures of maturing human small subunit (SSU) processomes at resolutions of 2.7 to 3.9 angstroms. These structures reveal the molecular mechanisms that enable crucial progressions during SSU processome maturation. RNA folding states within these particles are communicated to and coordinated with key enzymes that drive irreversible steps such as targeted exosome-mediated RNA degradation, protein-guided site-specific endonucleolytic RNA cleavage, and tightly controlled RNA unwinding. These conserved mechanisms highlight the SSU processome’s impressive structural plasticity, which endows this 4.5-megadalton nucleolar assembly with the distinctive ability to mature the small ribosomal subunit from within. | |||||||||
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_23938.map.gz | 619.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-23938-v30.xml emd-23938.xml | 118.9 KB 118.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_23938_fsc.xml | 19.7 KB | 表示 | FSCデータファイル |
画像 | emd_23938.png | 163.1 KB | ||
マスクデータ | emd_23938_msk_1.map | 669.9 MB | マスクマップ | |
その他 | emd_23938_additional_1.map.gz emd_23938_half_map_1.map.gz emd_23938_half_map_2.map.gz | 616.4 MB 536.2 MB 536.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23938 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23938 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_23938_validation.pdf.gz | 842.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_23938_full_validation.pdf.gz | 842 KB | 表示 | |
XML形式データ | emd_23938_validation.xml.gz | 27.8 KB | 表示 | |
CIF形式データ | emd_23938_validation.cif.gz | 37.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23938 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23938 | HTTPS FTP |
-関連構造データ
関連構造データ | 7mqaMC 7mq8C 7mq9C 7mqjC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10781 (タイトル: Nucleolar maturation of the human small subunit processome Data size: 74.6 TB Data #1: Unaligned multi-frame micrograph movies of human SSU processomes - Dataset 1 [micrographs - multiframe] Data #2: Unaligned multi-frame micrograph movies of human SSU processomes - Dataset 2 [micrographs - multiframe] Data #3: Unaligned multi-frame micrograph movies of human SSU processomes - Dataset 3 [micrographs - multiframe] Data #4: Unaligned multi-frame micrograph movies of human SSU processomes - Dataset 4 [micrographs - multiframe] Data #5: Unaligned multi-frame micrograph movies of human SSU processomes - Dataset 5 [micrographs - multiframe] Data #6: Unaligned multi-frame micrograph movies of human SSU processomes - Dataset 6 [micrographs - multiframe] Data #7: Aligned and averaged micrographs of human SSU processomes - Dataset 1 [micrographs - single frame] Data #8: Aligned and averaged micrographs of human SSU processomes - Dataset 2 [micrographs - single frame] Data #9: Aligned and averaged micrographs of human SSU processomes - Dataset 3 [micrographs - single frame] Data #10: Aligned and averaged micrographs of human SSU processomes - Dataset 4 [micrographs - single frame] Data #11: Aligned and averaged micrographs of human SSU processomes - Dataset 5 [micrographs - single frame] Data #12: Aligned and averaged micrographs of human SSU processomes - Dataset 6 [micrographs - single frame]) |
-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_23938.map.gz / 形式: CCP4 / 大きさ: 669.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.08 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
-マスク #1
ファイル | emd_23938_msk_1.map | ||||||||||||
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密度ヒストグラム |
-追加マップ: #1
ファイル | emd_23938_additional_1.map | ||||||||||||
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_23938_half_map_1.map | ||||||||||||
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_23938_half_map_2.map | ||||||||||||
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密度ヒストグラム |
-試料の構成要素
+全体 : Human SSU processome
+超分子 #1: Human SSU processome
+分子 #1: 5'ETS rRNA
+分子 #2: 18S rRNA
+分子 #3: U3 snoRNA
+分子 #4: 40S ribosomal protein S18
+分子 #5: 40S ribosomal protein S4, X isoform
+分子 #6: 40S ribosomal protein S5
+分子 #7: 40S ribosomal protein S6
+分子 #8: 40S ribosomal protein S7
+分子 #9: 40S ribosomal protein S8
+分子 #10: 40S ribosomal protein S9
+分子 #11: 40S ribosomal protein S12
+分子 #12: 40S ribosomal protein S16
+分子 #13: 40S ribosomal protein S11
+分子 #14: 40S ribosomal protein S24
+分子 #15: 40S ribosomal protein S28
+分子 #16: WD repeat-containing protein 75
+分子 #17: Nucleolar protein 11
+分子 #18: U3 small nucleolar RNA-associated protein 15 homolog
+分子 #19: WD repeat-containing protein 43
+分子 #20: HEAT repeat-containing protein 1
+分子 #21: U3 small nucleolar RNA-associated protein 4 homolog
+分子 #22: Periodic tryptophan protein 2 homolog
+分子 #23: U3 small nucleolar RNA-associated protein 6 homolog
+分子 #24: WD repeat-containing protein 3
+分子 #25: Transducin beta-like protein 3
+分子 #26: U3 small nucleolar RNA-associated protein 18 homolog
+分子 #27: WD repeat-containing protein 36
+分子 #28: DDB1- and CUL4-associated factor 13
+分子 #29: WD repeat-containing protein 46
+分子 #30: Active regulator of SIRT1
+分子 #31: U3 small nucleolar ribonucleoprotein protein IMP3
+分子 #32: U3 small nucleolar ribonucleoprotein protein MPP10
+分子 #33: Something about silencing protein 10
+分子 #34: Nucleolar protein 7
+分子 #35: 40S ribosomal protein S13
+分子 #36: 40S ribosomal protein S14
+分子 #37: Nucleolar protein 6
+分子 #38: Ribosomal RNA-processing protein 7 homolog A
+分子 #39: Probable dimethyladenosine transferase
+分子 #40: 40S ribosomal protein S3a
+分子 #41: 40S ribosomal protein S15a
+分子 #42: 40S ribosomal protein S19
+分子 #43: 40S ribosomal protein S27
+分子 #44: RRP12-like protein
+分子 #45: Probable ATP-dependent RNA helicase DHX37
+分子 #46: Ubiquitin-40S ribosomal protein S27a
+分子 #47: 40S ribosomal protein S17
+分子 #48: Exosome component 10
+分子 #49: Nucleolar protein 56
+分子 #50: Nucleolar protein 58
+分子 #51: rRNA 2'-O-methyltransferase fibrillarin
+分子 #52: NHP2-like protein 1
+分子 #53: U3 small nucleolar RNA-interacting protein 2
+分子 #54: RNA 3'-terminal phosphate cyclase-like protein
+分子 #55: Ribosome biogenesis protein BMS1 homolog
+分子 #56: Ribosomal RNA small subunit methyltransferase NEP1
+分子 #57: rRNA-processing protein FCF1 homolog
+分子 #58: U3 small nucleolar ribonucleoprotein protein IMP4
+分子 #59: Small subunit processome component 20 homolog
+分子 #60: Deoxynucleotidyltransferase terminal-interacting protein 2
+分子 #61: 40S ribosomal protein S23
+分子 #62: U3 small nucleolar RNA-associated protein 14 homolog A
+分子 #63: Nucleolar protein 14
+分子 #64: Nucleolar complex protein 4 homolog
+分子 #65: RNA-binding protein PNO1
+分子 #66: Unassigned peptides
+分子 #67: Probable U3 small nucleolar RNA-associated protein 11
+分子 #68: Bystin
+分子 #69: MAGNESIUM ION
+分子 #70: ADENOSINE-5'-TRIPHOSPHATE
+分子 #71: ZINC ION
+分子 #72: GUANOSINE-5'-TRIPHOSPHATE
+分子 #73: S-ADENOSYL-L-HOMOCYSTEINE
-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: 7.6 |
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グリッド | モデル: Quantifoil R2/2 / 材質: GOLD / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 支持フィルム - Film thickness: 3.0 nm / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 283 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 実像数: 84904 / 平均電子線量: 58.0 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 / Cs: 0.01 mm / 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): 0.7000000000000001 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |