+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-6864 | ||||||||||||
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タイトル | The Cryo-EM Structure of Human Catalytic Step I Spliceosome (C complex) at 4.1 angstrom resolution | ||||||||||||
マップデータ | |||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 exon-exon junction subcomplex mago-y14 / post-spliceosomal complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / snRNP binding / U2 snRNP binding / post-mRNA release spliceosomal complex ...exon-exon junction subcomplex mago-y14 / post-spliceosomal complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / cellular response to selenite ion / selenocysteine insertion sequence binding / exon-exon junction complex / snRNP binding / U2 snRNP binding / post-mRNA release spliceosomal complex / U7 snRNA binding / intracellular mRNA localization / histone pre-mRNA DCP binding / regulation of retinoic acid receptor signaling pathway / U7 snRNP / 3'-5' RNA helicase activity / regulation of translation at postsynapse, modulating synaptic transmission / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / generation of catalytic spliceosome for first transesterification step / negative regulation of excitatory postsynaptic potential / 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 / regulation of mRNA processing / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / Deadenylation of mRNA / embryonic brain development / methylosome / protein methylation / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / pre-mRNA binding / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U1 snRNP binding / RNA splicing, via transesterification reactions / Prp19 complex / poly(A) binding / positive regulation of androgen receptor activity / spliceosomal tri-snRNP complex / U4 snRNP / small nuclear ribonucleoprotein complex / M-decay: degradation of maternal mRNAs by maternally stored factors / P granule / RNA stem-loop binding / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / mRNA 3'-end processing / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / U2-type spliceosomal complex / embryonic cranial skeleton morphogenesis / telomerase RNA binding / telomerase holoenzyme complex / U2-type precatalytic spliceosome / regulation of mRNA splicing, via spliceosome / C2H2 zinc finger domain binding / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / positive regulation by host of viral transcription / Transport of Mature mRNA derived from an Intron-Containing Transcript / positive regulation of vitamin D receptor signaling pathway / U2 snRNP / Notch binding / nuclear vitamin D receptor binding / RNA Polymerase II Transcription Termination / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U1 snRNP / RUNX3 regulates NOTCH signaling / U2-type prespliceosome / NOTCH4 Intracellular Domain Regulates Transcription / K63-linked polyubiquitin modification-dependent protein binding / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / ubiquitin-ubiquitin ligase activity / exploration behavior / lipid biosynthetic process / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription / positive regulation of neurogenesis / precatalytic spliceosome / spliceosomal complex assembly / regulation of alternative mRNA splicing, via spliceosome / nuclear androgen receptor binding / cyclosporin A binding / Notch-HLH transcription pathway / mRNA Splicing - Minor Pathway / Formation of paraxial mesoderm / generation of catalytic spliceosome for second transesterification step / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / protein K63-linked ubiquitination / mitotic G2 DNA damage checkpoint signaling / negative regulation of DNA damage response, signal transduction by p53 class mediator / mRNA 3'-splice site recognition / 学習 / blastocyst development 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: 4.1 Å | ||||||||||||
データ登録者 | Zhan X / Yan C / Zhang X / Lei J / Shi Y | ||||||||||||
資金援助 | 中国, 3件
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引用 | ジャーナル: Science / 年: 2018 タイトル: Structure of a human catalytic step I spliceosome. 著者: Xiechao Zhan / Chuangye Yan / Xiaofeng Zhang / Jianlin Lei / Yigong Shi / 要旨: Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo-electron ...Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo-electron microscopy structure of the human C complex at an average resolution of 4.1 angstroms. Compared with the C complex, the human complex contains 11 additional proteins. The step I splicing factors CCDC49 and CCDC94 (Cwc25 and Yju2 in , respectively) closely interact with the DEAH-family adenosine triphosphatase/helicase Prp16 and bridge the gap between Prp16 and the active-site RNA elements. These features, together with structural comparison of the human C and C* complexes, provide mechanistic insights into ribonucleoprotein remodeling and allow the proposition of a working mechanism for the C-to-C* transition. | ||||||||||||
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_6864.map.gz | 228.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-6864-v30.xml emd-6864.xml | 76.8 KB 76.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_6864.png | 296.8 KB | ||
その他 | emd_6864_additional.map.gz emd_6864_half_map_1.map.gz emd_6864_half_map_2.map.gz | 223.7 MB 193.9 MB 193.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-6864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6864 | 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_6864.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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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:
CCP4マップ ヘッダ情報:
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-添付データ
-追加マップ: #1
ファイル | emd_6864_additional.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: #1
ファイル | emd_6864_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_6864_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 |
-試料の構成要素
+全体 : Human Catalytic Step I Spliceosome
+超分子 #1: Human Catalytic Step I Spliceosome
+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 200 kDa helicase
+分子 #5: 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 ISY1 homolog
+分子 #14: Pre-mRNA-splicing factor SYF2
+分子 #15: Protein BUD31 homolog
+分子 #16: Pre-mRNA-splicing factor RBM22
+分子 #17: Spliceosome-associated protein CWC15 homolog
+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: Intron-binding protein aquarius
+分子 #22: Serine/arginine repetitive matrix protein 2
+分子 #23: Pre-mRNA-splicing factor CWC22 homolog
+分子 #24: Pre-mRNA-processing factor 17
+分子 #25: Pre-mRNA-splicing factor CWC25 homolog
+分子 #26: Coiled-coil domain-containing protein 94
+分子 #27: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
+分子 #28: Pre-mRNA-processing factor 19
+分子 #29: Eukaryotic initiation factor 4A-III
+分子 #30: Protein mago nashi homolog 2
+分子 #31: RNA-binding protein 8A
+分子 #32: Protein CASC3
+分子 #33: Small nuclear ribonucleoprotein Sm D3
+分子 #34: Small nuclear ribonucleoprotein-associated proteins B and B'
+分子 #35: Small nuclear ribonucleoprotein Sm D1
+分子 #36: Small nuclear ribonucleoprotein Sm D2
+分子 #37: Small nuclear ribonucleoprotein F
+分子 #38: Small nuclear ribonucleoprotein E
+分子 #39: Small nuclear ribonucleoprotein G
+分子 #40: U2 small nuclear ribonucleoprotein A'
+分子 #41: U2 small nuclear ribonucleoprotein B''
+分子 #42: Peptidyl-prolyl cis-trans isomerase E
+分子 #43: Peptidylprolyl isomerase domain and WD repeat-containing protein 1
+分子 #44: Peptidyl-prolyl cis-trans isomerase G
+分子 #45: UNKNOW
+分子 #2: U5 snRNA
+分子 #6: U6 snRNA
+分子 #7: Pre-mRNA
+分子 #8: U2 snRNA
+分子 #46: INOSITOL HEXAKISPHOSPHATE
+分子 #47: GUANOSINE-5'-TRIPHOSPHATE
+分子 #48: MAGNESIUM ION
+分子 #49: ADENOSINE-5'-DIPHOSPHATE
+分子 #50: ZINC ION
+分子 #51: 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 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
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
粒子像選択 | 選択した数: 1464033 |
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CTF補正 | ソフトウェア - 名称: Gctf (ver. 0.66) |
初期 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION (ver. 2.0) |
最終 3次元分類 | ソフトウェア - 名称: RELION (ver. 2.0) |
最終 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION (ver. 2.0) |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: FOURIER SPACE / 解像度のタイプ: BY AUTHOR / 解像度: 4.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 2.0) / 使用した粒子像数: 53633 |