+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-32319 | |||||||||
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タイトル | The cryo-EM structure of human pre-C*-II complex | |||||||||
マップデータ | The cryo-EM map of human pre-C*-II complex | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 second spliceosomal transesterification activity / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / spliceosomal complex disassembly / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / pre-mRNA 3'-splice site binding / snRNP binding ...second spliceosomal transesterification activity / exon-exon junction subcomplex mago-y14 / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / spliceosomal complex disassembly / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / pre-mRNA 3'-splice site binding / snRNP binding / post-mRNA release spliceosomal complex / negative regulation of proteasomal protein catabolic process / U2 snRNP binding / regulation of retinoic acid receptor signaling pathway / negative regulation of toll-like receptor signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding / intracellular mRNA localization / regulation of translation at postsynapse, modulating synaptic transmission / 3'-5' RNA helicase activity / U7 snRNP / generation of catalytic spliceosome for first transesterification step / renal system process / negative regulation of excitatory postsynaptic potential / histone pre-mRNA 3'end processing complex / alternative mRNA splicing, via spliceosome / regulation of vitamin D receptor signaling pathway / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / negative regulation of interleukin-8 production / regulation of mRNA processing / negative regulation of lipopolysaccharide-mediated signaling pathway / Deadenylation of mRNA / embryonic brain development / negative regulation of phosphorylation / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / negative regulation of interferon-beta production / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / U1 snRNP binding / pICln-Sm protein complex / Prp19 complex / RNA splicing, via transesterification reactions / poly(A) binding / positive regulation of androgen receptor activity / M-decay: degradation of maternal mRNAs by maternally stored factors / RNA stem-loop binding / mRNA 3'-end processing / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / pre-mRNA binding / sno(s)RNA-containing ribonucleoprotein complex / ATP-dependent activity, acting on RNA / SMN-Sm protein complex / embryonic cranial skeleton morphogenesis / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / telomerase holoenzyme complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / commitment complex / positive regulation by host of viral transcription / U4 snRNP / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / Notch binding / U2 snRNP / nuclear vitamin D receptor binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RNA Polymerase II Transcription Termination / RUNX3 regulates NOTCH signaling / U1 snRNP / NOTCH4 Intracellular Domain Regulates Transcription / U2-type prespliceosome / ubiquitin-ubiquitin ligase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / K63-linked polyubiquitin modification-dependent protein binding / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / exploration behavior / positive regulation of neurogenesis / lipid biosynthetic process / precatalytic spliceosome / nuclear androgen receptor binding / cyclosporin A binding / negative regulation of type I interferon-mediated signaling pathway / regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / negative regulation of NF-kappaB transcription factor activity / protein kinase inhibitor activity 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / human (ヒト) / unidentified adenovirus (ウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å | |||||||||
データ登録者 | Zhan X / Lu Y / Shi Y | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Mol Cell / 年: 2022 タイトル: Mechanism of exon ligation by human spliceosome. 著者: Xiechao Zhan / Yichen Lu / Xiaofeng Zhang / Chuangye Yan / Yigong Shi / 要旨: Pre-mRNA splicing involves two sequential reactions: branching and exon ligation. The C complex after branching undergoes remodeling to become the C complex, which executes exon ligation. Here, we ...Pre-mRNA splicing involves two sequential reactions: branching and exon ligation. The C complex after branching undergoes remodeling to become the C complex, which executes exon ligation. Here, we report cryo-EM structures of two intermediate human spliceosomal complexes, pre-C-I and pre-C-II, both at 3.6 Å. In both structures, the 3' splice site is already docked into the active site, the ensuing 3' exon sequences are anchored on PRP8, and the step II factor FAM192A contacts the duplex between U2 snRNA and the branch site. In the transition of pre-C-I to pre-C-II, the step II factors Cactin, FAM32A, PRKRIP1, and SLU7 are recruited. Notably, the RNA helicase PRP22 is positioned quite differently in the pre-C-I, pre-C-II, and C complexes, suggesting a role in 3' exon binding and proofreading. Together with information on human C and C complexes, our studies recapitulate a molecular choreography of the C-to-C transition, revealing mechanistic insights into exon ligation. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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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 | emd_32319.map.gz | 230.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-32319-v30.xml emd-32319.xml | 63.6 KB 63.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_32319.png | 68.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-32319 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32319 | HTTPS FTP |
-関連構造データ
関連構造データ | 7w5aMC 7w59C 7w5bC 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 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_32319.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 | The cryo-EM map of human pre-C*-II complex | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.338 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
-試料の構成要素
+全体 : Human pre-C*-II complex
+超分子 #1: Human pre-C*-II complex
+分子 #1: Pre-mRNA-processing-splicing factor 8
+分子 #3: 116 kDa U5 small nuclear ribonucleoprotein component
+分子 #4: U5 small nuclear ribonucleoprotein 40 kDa protein
+分子 #9: Pre-mRNA-splicing factor SYF1
+分子 #10: Crooked neck-like protein 1
+分子 #11: Pre-mRNA-splicing factor SPF27
+分子 #12: Cell division cycle 5-like protein
+分子 #13: Pre-mRNA-splicing factor SYF2
+分子 #14: Protein BUD31 homolog
+分子 #15: Pre-mRNA-splicing factor RBM22
+分子 #16: Spliceosome-associated protein CWC15 homolog
+分子 #17: RNA helicase aquarius
+分子 #18: SNW domain-containing protein 1
+分子 #19: Peptidyl-prolyl cis-trans isomerase-like 1
+分子 #20: Pleiotropic regulator 1
+分子 #21: Serine/arginine repetitive matrix protein 2
+分子 #22: Pre-mRNA-splicing factor CWC22 homolog
+分子 #23: Pre-mRNA-processing factor 17
+分子 #24: PSME3-interacting protein
+分子 #25: ATP-dependent RNA helicase DHX8
+分子 #26: Cactin
+分子 #27: PRKR-interacting protein 1
+分子 #28: Protein FAM32A
+分子 #29: Small nuclear ribonucleoprotein-associated proteins B and B'
+分子 #30: Peptidyl-prolyl cis-trans isomerase E
+分子 #31: Small nuclear ribonucleoprotein Sm D3
+分子 #32: Small nuclear ribonucleoprotein Sm D1
+分子 #33: Small nuclear ribonucleoprotein Sm D2
+分子 #34: Small nuclear ribonucleoprotein F
+分子 #35: Small nuclear ribonucleoprotein E
+分子 #36: Small nuclear ribonucleoprotein G
+分子 #37: Protein mago nashi homolog
+分子 #38: RNA-binding protein 8A
+分子 #39: Eukaryotic initiation factor 4A-III
+分子 #40: Protein CASC3
+分子 #41: Pre-mRNA-processing factor 19
+分子 #42: U2 small nuclear ribonucleoprotein A'
+分子 #43: U2 small nuclear ribonucleoprotein B''
+分子 #44: Pre-mRNA-splicing factor SLU7
+分子 #2: U5 snRNA
+分子 #5: U6 snRNA
+分子 #6: Pre-mRNA
+分子 #7: Pre-mRNA
+分子 #8: U2 snRNA
+分子 #45: INOSITOL HEXAKISPHOSPHATE
+分子 #46: GUANOSINE-5'-TRIPHOSPHATE
+分子 #47: MAGNESIUM ION
+分子 #48: ZINC ION
+分子 #49: ADENOSINE-5'-TRIPHOSPHATE
-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: 7.9 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.2 µm |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 50.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
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最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 212224 |