+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5z56 | ||||||||||||
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タイトル | cryo-EM structure of a human activated spliceosome (mature Bact) at 5.1 angstrom. | ||||||||||||
要素 |
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キーワード | SPLICING / human activated spliceosome / mature Bact / pre-mRNA splicing | ||||||||||||
機能・相同性 | 機能・相同性情報 RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / post-mRNA release spliceosomal complex / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step ...RES complex / negative regulation of chemokine-mediated signaling pathway / snoRNA splicing / U11/U12 snRNP / post-mRNA release spliceosomal complex / 3'-5' RNA helicase activity / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / generation of catalytic spliceosome for first transesterification step / 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 / embryonic brain development / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / miRNA processing / methylosome / Prp19 complex / 7-methylguanosine cap hypermethylation / positive regulation of androgen receptor activity / poly(A) binding / U1 snRNP binding / mRNA 3'-end processing / blastocyst formation / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / telomerase RNA binding / transcription regulator inhibitor activity / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / SAGA complex / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / ubiquitin-ubiquitin ligase activity / WD40-repeat domain binding / pattern recognition receptor activity / lipid biosynthetic process / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / positive regulation of transcription by RNA polymerase I / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of alternative mRNA splicing, via spliceosome / protein K63-linked ubiquitination / regulation of RNA splicing / antiviral innate immune response / blastocyst development / mRNA 3'-splice site recognition / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / proteasomal protein catabolic process / positive regulation of G1/S transition of mitotic cell cycle / U5 snRNP / transcription-coupled nucleotide-excision repair / positive regulation of viral genome replication / RNA processing / U2 snRNA binding / U6 snRNA binding / regulation of DNA repair / spliceosomal snRNP assembly / protein peptidyl-prolyl isomerization / Cajal body / pre-mRNA intronic binding / negative regulation of canonical NF-kappaB signal transduction / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / lipid droplet / mRNA Splicing - Major Pathway / RNA splicing / helicase activity 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) unidentified adenovirus (ウイルス) | ||||||||||||
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: 5.1 Å | ||||||||||||
データ登録者 | Zhang, X. / Yan, C. / Zhan, X. / Li, L. / Lei, J. / Shi, Y. | ||||||||||||
資金援助 | 中国, 3件
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引用 | ジャーナル: Cell Res / 年: 2018 タイトル: Structure of the human activated spliceosome in three conformational states. 著者: Xiaofeng Zhang / Chuangye Yan / Xiechao Zhan / Lijia Li / Jianlin Lei / Yigong Shi / 要旨: During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B complex), which has a well-formed active site but cannot proceed to ...During each cycle of pre-mRNA splicing, the pre-catalytic spliceosome (B complex) is converted into the activated spliceosome (B complex), which has a well-formed active site but cannot proceed to the branching reaction. Here, we present the cryo-EM structure of the human B complex in three distinct conformational states. The EM map allows atomic modeling of nearly all protein components of the U2 small nuclear ribonucleoprotein (snRNP), including three of the SF3a complex and seven of the SF3b complex. The structure of the human B complex contains 52 proteins, U2, U5, and U6 small nuclear RNA (snRNA), and a pre-mRNA. Three distinct conformations have been captured, representing the early, mature, and late states of the human B complex. These complexes differ in the orientation of the Switch loop of Prp8, the splicing factors RNF113A and NY-CO-10, and most components of the NineTeen complex (NTC) and the NTC-related complex. Analysis of these three complexes and comparison with the B and C complexes reveal an ordered flux of components in the B-to-B and the B-to-B transitions, which ultimately prime the active site for the branching reaction. | ||||||||||||
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 | 5z56.cif.gz | 3.4 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5z56.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 5z56.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 | 5z56_validation.pdf.gz | 1.9 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5z56_full_validation.pdf.gz | 2.4 MB | 表示 | |
XML形式データ | 5z56_validation.xml.gz | 433.4 KB | 表示 | |
CIF形式データ | 5z56_validation.cif.gz | 697.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/z5/5z56 ftp://data.pdbj.org/pub/pdb/validation_reports/z5/5z56 | HTTPS FTP |
-関連構造データ
-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 , 18種, 19分子 ACbi6JLQMNPRSTUXYZx
+RNA鎖 , 4種, 4分子 BFGH
+U5 small nuclear ribonucleoprotein ... , 2種, 2分子 DE
+Small nuclear ribonucleoprotein ... , 6種, 12分子 ahcjdkfmelgn
+U2 small nuclear ribonucleoprotein ... , 2種, 2分子 op
+Splicing factor 3A subunit ... , 3種, 3分子 wuv
+Splicing factor 3B subunit ... , 6種, 6分子 123457
+Pre-mRNA-processing factor ... , 2種, 5分子 qrstW
+Pre-mRNA-splicing factor ... , 4種, 4分子 KIOV
+Peptidyl-prolyl cis-trans isomerase ... , 2種, 2分子 zy
+非ポリマー , 4種, 21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 activated spliceosome / タイプ: COMPLEX / Entity ID: #1-#49 / 由来: NATURAL |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 7.9 / 詳細: 20 mM HEPES-KOH, 150 mM NaCl, 1.5 mM MgCl2 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
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: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / アライメント法: BASIC |
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 | 電子線照射量: 48 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | タイプ: NONE | ||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||
3次元再構成 | 解像度: 5.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 27405 / アルゴリズム: FOURIER SPACE / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||
精密化 | 最高解像度: 5.1 Å |