+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 6qx9 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Structure of a human fully-assembled precatalytic spliceosome (pre-B complex). | |||||||||
![]() |
| |||||||||
![]() | SPLICING / RNP complex / RNA / protein / spliceosome | |||||||||
機能・相同性 | ![]() mRNA Splicing - Minor Pathway / negative regulation of protein refolding / mRNA Splicing - Major Pathway / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA ...mRNA Splicing - Minor Pathway / negative regulation of protein refolding / mRNA Splicing - Major Pathway / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / positive regulation of hippo signaling / RNA localization / R-loop processing / U4atac snRNA binding / regulation of ATP-dependent activity / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / regulation of mitotic cell cycle spindle assembly checkpoint / U6 snRNP / box C/D sno(s)RNA binding / U11/U12 snRNP / PH domain binding / dense fibrillar component / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / snRNP binding / U1 snRNP binding / P-body assembly / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / U2-type catalytic step 1 spliceosome / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / SMN-Sm protein complex / negative regulation of chaperone-mediated autophagy / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / telomerase RNA binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / positive regulation of mRNA splicing, via spliceosome / box C/D snoRNP assembly / U4 snRNP / rRNA modification in the nucleus and cytosol / U2 snRNP / RNA Polymerase II Transcription Termination / SAGA complex / U3 snoRNA binding / positive regulation of transcription by RNA polymerase III / U1 snRNP / pre-mRNA 5'-splice site binding / tRNA processing / Cajal body / U2-type prespliceosome / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / mRNA catabolic process / mRNA 5'-splice site recognition / nuclear-transcribed mRNA catabolic process / mRNA 3'-splice site recognition / MLL1 complex / spliceosomal tri-snRNP complex assembly / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / U2 snRNA binding / RNA processing / U6 snRNA binding / ribonucleoprotein complex binding / spliceosomal snRNP assembly / regulation of DNA repair / pre-mRNA intronic binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.28 Å | |||||||||
![]() | Charenton, C. / Wilkinson, M.E. / Nagai, K. | |||||||||
資金援助 | ![]()
| |||||||||
![]() | ![]() タイトル: Mechanism of 5' splice site transfer for human spliceosome activation. 著者: Clément Charenton / Max E Wilkinson / Kiyoshi Nagai / ![]() 要旨: The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 ...The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 tri-snRNP to form the fully assembled precatalytic pre-B spliceosome. Here, we report cryo-electron microscopy structures of the human pre-B complex captured before U1 snRNP dissociation at 3.3-angstrom core resolution and the human tri-snRNP at 2.9-angstrom resolution. U1 snRNP inserts the 5'SS-U1 snRNA helix between the two RecA domains of the Prp28 DEAD-box helicase. Adenosine 5'-triphosphate-dependent closure of the Prp28 RecA domains releases the 5'SS to pair with the nearby U6 ACAGAGA-box sequence presented as a mobile loop. The structures suggest that formation of the 5'SS-ACAGAGA helix triggers remodeling of an intricate protein-RNA network to induce Brr2 helicase relocation to its loading sequence in U4 snRNA, enabling Brr2 to unwind the U4/U6 snRNA duplex to allow U6 snRNA to form the catalytic center of the spliceosome. | |||||||||
履歴 |
|
-
構造の表示
ムービー |
![]() |
---|---|
構造ビューア | 分子: ![]() ![]() |
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 3.2 MB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 表示 | ![]() | |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
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 | ![]() 4665MC ![]() 4658C ![]() 4672C ![]() 4673C ![]() 4674C ![]() 4675C ![]() 4676C ![]() 4686C ![]() 4687C ![]() 4688C ![]() 4689C ![]() 4690C ![]() 6qw6C M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
---|---|
類似構造データ | |
電子顕微鏡画像生データ | ![]() Data size: 2.3 TB Data #1: Dataset 1 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #2: Dataset 2 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #3: Dataset 3 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #4: Dataset 4 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #5: Dataset 5 of human pre-B spliceosome; motion-corrected micrographs [micrographs - single frame] Data #6: Selected U4/U6.U5 tri-snRNP particles after Bayesian polishing [picked particles - single frame - processed] Data #7: Crude shifted preB particles [picked particles - single frame - unprocessed]) |
-
リンク
-
集合体
登録構造単位 | ![]()
|
---|---|
1 |
|
-
要素
+RNA鎖 , 6種, 6分子 16I524
+U5 small nuclear ribonucleoprotein ... , 2種, 2分子 5O5B
+Splicing factor 3B subunit ... , 5種, 5分子 B4B2B5B3B1
+Small nuclear ribonucleoprotein ... , 6種, 24分子 135323435e4e1e2e411151211f2f5f4f224252121g2g5g4g
+U4/U6 small nuclear ribonucleoprotein ... , 3種, 3分子 4B4C4A
+U1 small nuclear ribonucleoprotein ... , 3種, 3分子 1K1A1C
+タンパク質 , 11種, 14分子 RX5C5X1b2b5b4b5J4D5A5DBPK
+U6 snRNA-associated Sm-like protein ... , 7種, 7分子 66676263686465
+U2 small nuclear ribonucleoprotein ... , 2種, 2分子 2B2A
+Splicing factor 3A subunit ... , 3種, 3分子 A2A3A1
+U4/U6.U5 tri-snRNP-associated protein ... , 2種, 2分子 SU
+非ポリマー , 4種, 9分子 ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/IHP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/IHP.gif)
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-
試料調製
構成要素 |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
分子量 | 値: 3.0 MDa / 実験値: NO | ||||||||||||||||||||||||||||||
由来(天然) |
| ||||||||||||||||||||||||||||||
由来(組換発現) |
| ||||||||||||||||||||||||||||||
緩衝液 | pH: 7.9 | ||||||||||||||||||||||||||||||
緩衝液成分 |
| ||||||||||||||||||||||||||||||
試料 | 濃度: 1.4 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Quantifoil R2/2 | ||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
-
電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 6 sec. / 電子線照射量: 50 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
電子光学装置 | エネルギーフィルター名称: GIF Bioquantum / エネルギーフィルタースリット幅: 20 eV |
画像スキャン | 動画フレーム数/画像: 40 / 利用したフレーム数/画像: 1-40 |
-
解析
EMソフトウェア |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 1130953 | ||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.28 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 86146 / アルゴリズム: FOURIER SPACE / 対称性のタイプ: POINT |