+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-6839 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom | ||||||||||||
マップデータ | Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom | ||||||||||||
試料 |
| ||||||||||||
キーワード | Post-catalytic Spliceosome (P complex) / RNA splicing / exon ligation / spliceosome / SPLICING | ||||||||||||
機能・相同性 | 機能・相同性情報 U2-type post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / mRNA branch site recognition / spliceosomal complex disassembly / cellular bud site selection / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / nuclear mRNA surveillance / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome ...U2-type post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / mRNA branch site recognition / spliceosomal complex disassembly / cellular bud site selection / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / nuclear mRNA surveillance / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / 7-methylguanosine cap hypermethylation / Prp19 complex / snRNP binding / pICln-Sm protein complex / small nuclear ribonucleoprotein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / SMN-Sm protein complex / spliceosomal tri-snRNP complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / poly(U) RNA binding / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / Formation of TC-NER Pre-Incision Complex / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA replication origin binding / mRNA 5'-splice site recognition / protein K63-linked ubiquitination / mRNA 3'-splice site recognition / Dual incision in TC-NER / DNA replication initiation / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / positive regulation of cell cycle / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / nuclear periphery / positive regulation of RNA splicing / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / RNA helicase activity / RNA helicase / DNA repair / GTPase activity / mRNA binding / chromatin binding / chromatin / GTP binding / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||||||||
生物種 | Saccharomyces cerevisiae S288c (パン酵母) | ||||||||||||
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 | Wan R / Yan C | ||||||||||||
資金援助 | 中国, 3件
| ||||||||||||
引用 | ジャーナル: Cell / 年: 2017 タイトル: Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae. 著者: Rui Bai / Chuangye Yan / Ruixue Wan / Jianlin Lei / Yigong Shi / 要旨: Removal of an intron from a pre-mRNA by the spliceosome results in the ligation of two exons in the post-catalytic spliceosome (known as the P complex). Here, we present a cryo-EM structure of the ...Removal of an intron from a pre-mRNA by the spliceosome results in the ligation of two exons in the post-catalytic spliceosome (known as the P complex). Here, we present a cryo-EM structure of the P complex from Saccharomyces cerevisiae at an average resolution of 3.6 Å. The ligated exon is held in the active site through RNA-RNA contacts. Three bases at the 3' end of the 5' exon remain anchored to loop I of U5 small nuclear RNA, and the conserved AG nucleotides of the 3'-splice site (3'SS) are specifically recognized by the invariant adenine of the branch point sequence, the guanine base at the 5' end of the 5'SS, and an adenine base of U6 snRNA. The 3'SS is stabilized through an interaction with the 1585-loop of Prp8. The P complex structure provides a view on splice junction formation critical for understanding the complete splicing cycle. | ||||||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_6839.map.gz | 228.8 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-6839-v30.xml emd-6839.xml | 57.3 KB 57.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_6839.png | 153.3 KB | ||
Filedesc metadata | emd-6839.cif.gz | 15.4 KB | ||
その他 | emd_6839_additional.map.gz | 228.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-6839 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6839 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_6839.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.6 angstrom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-追加マップ: Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces...
ファイル | emd_6839_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Cryo-EM Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae at 3.85 angstrom | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : the Post-catalytic Spliceosome (P complex)
+超分子 #1: the Post-catalytic Spliceosome (P complex)
+分子 #1: Pre-mRNA-splicing factor 8
+分子 #3: Pre-mRNA-splicing factor SNU114
+分子 #7: Pre-mRNA-splicing factor SNT309
+分子 #8: Pre-mRNA-splicing factor SYF1
+分子 #9: Pre-mRNA-splicing factor CLF1
+分子 #10: Pre-mRNA-splicing factor CEF1
+分子 #11: Pre-mRNA-splicing factor SYF2
+分子 #12: Pre-mRNA-splicing factor BUD31
+分子 #13: Pre-mRNA-processing factor 17
+分子 #14: Pre-mRNA-splicing factor SLT11
+分子 #15: Pre-mRNA-splicing factor CWC2
+分子 #16: Pre-mRNA-splicing factor PRP46
+分子 #17: Pre-mRNA-splicing factor CWC15
+分子 #18: Pre-mRNA-processing protein 45
+分子 #19: Pre-mRNA-splicing factor CWC21
+分子 #20: Pre-mRNA-splicing factor CWC22
+分子 #21: Pre-mRNA-splicing factor 18
+分子 #22: Pre-mRNA-splicing factor SLU7
+分子 #23: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22
+分子 #24: Small nuclear ribonucleoprotein-associated protein B
+分子 #25: Small nuclear ribonucleoprotein E
+分子 #26: Small nuclear ribonucleoprotein F
+分子 #27: Small nuclear ribonucleoprotein G
+分子 #28: Small nuclear ribonucleoprotein Sm D3
+分子 #29: Small nuclear ribonucleoprotein Sm D1
+分子 #30: Small nuclear ribonucleoprotein Sm D2
+分子 #31: U2 small nuclear ribonucleoprotein A'
+分子 #32: U2 small nuclear ribonucleoprotein B''
+分子 #33: Pre-mRNA-processing factor 19
+分子 #2: U5 snRNA
+分子 #4: U6 snRNA
+分子 #5: mRNA/intron lariat
+分子 #6: U2 snRNA
+分子 #34: INOSITOL HEXAKISPHOSPHATE
+分子 #35: GUANOSINE-5'-TRIPHOSPHATE
+分子 #36: MAGNESIUM ION
+分子 #37: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
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 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 50.0 e/Å2 |
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 FIELD / Cs: 2.7 mm |
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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |