+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6ff7 | ||||||
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タイトル | human Bact spliceosome core structure | ||||||
要素 |
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キーワード | SPLICING / spliceosome / human / HELA / BACT / dynamics | ||||||
機能・相同性 | 機能・相同性情報 post-spliceosomal complex / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding ...post-spliceosomal complex / RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / post-mRNA release spliceosomal complex / regulation of retinoic acid receptor signaling pathway / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / 3'-5' RNA helicase activity / U7 snRNP / generation of catalytic spliceosome for first transesterification step / B-WICH complex / regulation of vitamin D receptor signaling pathway / 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 / miRNA processing / splicing factor binding / protein methylation / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U12-type spliceosomal complex / embryonic brain development / methylosome / nuclear retinoic acid receptor binding / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / poly(A) binding / Prp19 complex / U1 snRNP binding / mRNA 3'-end processing / blastocyst formation / pICln-Sm protein complex / snRNP binding / sno(s)RNA-containing ribonucleoprotein complex / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / pre-mRNA binding / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / positive regulation by host of viral transcription / mRNA cis splicing, via spliceosome / positive regulation of vitamin D receptor signaling pathway / transcription regulator inhibitor activity / commitment complex / U2-type prespliceosome assembly / nuclear vitamin D receptor binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type catalytic step 2 spliceosome / Notch binding / SAGA complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / U4 snRNP / positive regulation of mRNA splicing, via spliceosome / RUNX3 regulates NOTCH signaling / RHOBTB1 GTPase cycle / U2 snRNP / RNA Polymerase II Transcription Termination / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / positive regulation of neurogenesis / pattern recognition receptor activity / NOTCH3 Intracellular Domain Regulates Transcription / WD40-repeat domain binding / lipid biosynthetic process / U2-type prespliceosome / nuclear androgen receptor binding / precatalytic spliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / positive regulation of transcription by RNA polymerase I / Notch-HLH transcription pathway / generation of catalytic spliceosome for second transesterification step / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / SMAD binding / regulation of RNA splicing / protein K63-linked ubiquitination / protein peptidyl-prolyl isomerization / mRNA 3'-splice site recognition / blastocyst development / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / transcription-coupled nucleotide-excision repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNA binding 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
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: 4.5 Å | ||||||
データ登録者 | Haselbach, D. / Komarov, I. / Agafonov, D. / Hartmuth, K. / Graf, B. / Kastner, B. / Luehrmann, R. / Stark, H. | ||||||
引用 | ジャーナル: Cell / 年: 2018 タイトル: Structure and Conformational Dynamics of the Human Spliceosomal B Complex. 著者: David Haselbach / Ilya Komarov / Dmitry E Agafonov / Klaus Hartmuth / Benjamin Graf / Olexandr Dybkov / Henning Urlaub / Berthold Kastner / Reinhard Lührmann / Holger Stark / 要旨: The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B spliceosome at 3.4 Å resolution. In ...The spliceosome is a highly dynamic macromolecular complex that precisely excises introns from pre-mRNA. Here we report the cryo-EM 3D structure of the human B spliceosome at 3.4 Å resolution. In the B state, the spliceosome is activated but not catalytically primed, so that it is functionally blocked prior to the first catalytic step of splicing. The spliceosomal core is similar to the yeast B spliceosome; important differences include the presence of the RNA helicase aquarius and peptidyl prolyl isomerases. To examine the overall dynamic behavior of the purified spliceosome, we developed a principal component analysis-based approach. Calculating the energy landscape revealed eight major conformational states, which we refined to higher resolution. Conformational differences of the highly flexible structural components between these eight states reveal how spliceosomal components contribute to the assembly of the spliceosome, allowing it to generate a dynamic interaction network required for its subsequent catalytic activation. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6ff7.cif.gz | 2.8 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6ff7.ent.gz | 1.8 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6ff7.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 6ff7_validation.pdf.gz | 1.6 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6ff7_full_validation.pdf.gz | 1.7 MB | 表示 | |
XML形式データ | 6ff7_validation.xml.gz | 301.2 KB | 表示 | |
CIF形式データ | 6ff7_validation.cif.gz | 543.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ff/6ff7 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/6ff7 | HTTPS FTP |
-関連構造データ
関連構造データ | 4240MC 4233C 4234C 4235C 4236C 4237C 4238C 4239C 4247C 4248C 4249C 4250C 4251C 4252C 4253C 4254C 4255C 6ff4C 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 (文献) |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10160 (タイトル: Conformational Dynamics of human Bact spliceosome Data size: 2.8 TB Data #1: aligned and summed micrograph stack of human Bact spliceosome [micrographs - single frame] Data #2: aligned, dose-weighted and summed micrograph stack of human Bact spliceosome [micrographs - single frame]) |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
+タンパク質 , 17種, 18分子 13ABCDLOQRVty0Ufmq
+RNA鎖 , 4種, 4分子 256Z
+Splicing factor 3A subunit ... , 3種, 3分子 79p
+Splicing factor 3B subunit ... , 5種, 6分子 8uvxzN
+Pre-mRNA-processing factor ... , 2種, 5分子 EGHIJ
+Pre-mRNA-splicing factor ... , 5種, 5分子 PKMTw
+Serine/arginine repetitive matrix protein ... , 2種, 2分子 SY
+Peptidyl-prolyl cis-trans isomerase ... , 2種, 2分子 so
+U5 small nuclear ribonucleoprotein ... , 2種, 2分子 Fr
+U2 small nuclear ribonucleoprotein ... , 2種, 2分子 WX
+Small nuclear ribonucleoprotein ... , 6種, 12分子 ahbicjdkelgn
+非ポリマー , 5種, 20分子
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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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 | 名称: human Bact spliceosome / タイプ: COMPLEX / Entity ID: #1-#50 / 由来: NATURAL |
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分子量 | 実験値: NO |
由来(天然) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 7.6 |
試料 | 包埋: YES / 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: 200 divisions/in. / グリッドのタイプ: Quantifoil R3.5/1 |
EM embedding | Material: ice |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 40 e/Å2 / 検出モード: INTEGRATING フィルム・検出器のモデル: FEI FALCON III (4k x 4k) |
画像スキャン | サンプリングサイズ: 14 µm / 横: 4096 / 縦: 4096 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING ONLY | ||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||
3次元再構成 | 解像度: 4.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 165853 / 対称性のタイプ: POINT |