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基本情報
登録情報 | データベース: EMDB / ID: EMD-9524 | |||||||||
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タイトル | Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution | |||||||||
![]() | Cryo-EM map of Bact spliceosome at 3.5-angstrom resolution | |||||||||
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機能・相同性 | ![]() U2-type post-mRNA release spliceosomal complex / RES complex / maintenance of RNA location / mRNA branch site recognition / snoRNA splicing / cellular bud site selection / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step ...U2-type post-mRNA release spliceosomal complex / RES complex / maintenance of RNA location / mRNA branch site recognition / snoRNA splicing / cellular bud site selection / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / cis assembly of pre-catalytic spliceosome / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / miRNA processing / U4/U6 snRNP / Prp19 complex / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / ATP-dependent activity, acting on RNA / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome assembly / poly(U) RNA binding / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / 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 / spliceosomal tri-snRNP complex assembly / DNA replication initiation / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / protein peptidyl-prolyl isomerization / mRNA export from nucleus / positive regulation of cell cycle / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / nuclear periphery / helicase activity / positive regulation of RNA splicing / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA processing / mRNA splicing, via spliceosome / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / nucleic acid binding / RNA helicase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA helicase / nuclear speck / response to xenobiotic stimulus / cell cycle / DNA repair / GTPase activity / mRNA binding / chromatin binding / chromatin / nucleolus / GTP binding / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | |||||||||
![]() | Yan C / Wan R / Bai R / Huang G / Shi Y | |||||||||
![]() | ![]() タイトル: Structure of a yeast activated spliceosome at 3.5 Å resolution. 著者: Chuangye Yan / Ruixue Wan / Rui Bai / Gaoxingyu Huang / Yigong Shi / ![]() 要旨: Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome ...Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome (known as the B(act) complex) from Saccharomyces cerevisiae, determined by cryo-electron microscopy at an average resolution of 3.52 angstroms. The final refined model contains U2 and U5 small nuclear ribonucleoprotein particles (snRNPs), U6 small nuclear RNA (snRNA), nineteen complex (NTC), NTC-related (NTR) protein, and a 71-nucleotide pre-mRNA molecule, which amount to 13,505 amino acids from 38 proteins and a combined molecular mass of about 1.6 megadaltons. The 5' exon is anchored by loop I of U5 snRNA, whereas the 5' splice site (5'SS) and the branch-point sequence (BPS) of the intron are specifically recognized by U6 and U2 snRNA, respectively. Except for coordination of the catalytic metal ions, the RNA elements at the catalytic cavity of Prp8 are mostly primed for catalysis. The catalytic latency is maintained by the SF3b complex, which encircles the BPS, and the splicing factors Cwc24 and Prp11, which shield the 5' exon-5'SS junction. This structure, together with those determined earlier, outlines a molecular framework for the pre-mRNA splicing reaction. | |||||||||
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構造の表示
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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-検証レポート
文書・要旨 | ![]() | 553.1 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 552.7 KB | 表示 | |
XML形式データ | ![]() | 7.1 KB | 表示 | |
CIF形式データ | ![]() | 8.1 KB | 表示 | |
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「今月の分子」の関連する項目 |
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マップ
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注釈 | Cryo-EM map of Bact spliceosome at 3.5-angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.306 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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試料の構成要素
+全体 : Bact spliceosomal complex
+超分子 #1: Bact spliceosomal complex
+分子 #1: Pre-mRNA-splicing factor 8
+分子 #2: Pre-mRNA-splicing helicase BRR2
+分子 #3: Pre-mRNA-splicing factor SNU114
+分子 #6: Pre-mRNA-splicing factor RSE1
+分子 #7: Cold sensitive U2 snRNA suppressor 1
+分子 #8: Pre-mRNA-splicing factor PRP11
+分子 #9: Pre-mRNA-splicing factor RDS3
+分子 #10: RDS3 complex subunit 10
+分子 #14: Pre-mRNA-splicing factor PRP46
+分子 #15: Pre-mRNA-processing protein 45
+分子 #16: Pre-mRNA-splicing factor SLT11
+分子 #17: Pre-mRNA-splicing factor CWC2
+分子 #18: Pre-mRNA-splicing factor CWC15
+分子 #19: Pre-mRNA-splicing factor BUD31
+分子 #20: Pre-mRNA leakage protein 1
+分子 #21: U2 snRNP component IST3
+分子 #22: Pre-mRNA-splicing factor CWC26
+分子 #23: Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2
+分子 #24: Pre-mRNA-splicing factor CWC22
+分子 #25: Pre-mRNA-splicing factor CWC24
+分子 #26: Peptidyl-prolyl isomerase CWC27
+分子 #27: Pre-mRNA-splicing factor CEF1
+分子 #28: U2 snRNP component HSH155
+分子 #29: Pre-mRNA-splicing factor CLF1
+分子 #30: Pre-mRNA-splicing factor CWC21
+分子 #31: Pre-mRNA-splicing factor SYF1
+分子 #32: Protein HSH49
+分子 #33: Pre-mRNA-splicing factor SYF2
+分子 #34: Pre-mRNA-processing factor 19
+分子 #35: Pre-mRNA-splicing factor SNT309
+分子 #36: Pre-mRNA-processing factor 17
+分子 #37: Small nuclear ribonucleoprotein-associated protein B
+分子 #38: Small nuclear ribonucleoprotein E
+分子 #39: Small nuclear ribonucleoprotein F
+分子 #40: Small nuclear ribonucleoprotein G
+分子 #41: Small nuclear ribonucleoprotein Sm D3
+分子 #42: Small nuclear ribonucleoprotein Sm D1
+分子 #43: Small nuclear ribonucleoprotein Sm D2
+分子 #4: Saccharomyces cerevisiae strain CDRDR_sf_H chromosome VII sequence
+分子 #5: Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence
+分子 #11: U2 snRNA
+分子 #12: Pre-mRNA
+分子 #13: Pre-mRNA
+分子 #44: GUANOSINE-5'-TRIPHOSPHATE
+分子 #45: MAGNESIUM ION
+分子 #46: ZINC ION
+分子 #47: ADENOSINE-5'-DIPHOSPHATE
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 8 詳細: CEB buffer (10 mM Tris-HCl, pH 8.0, 75 mM NaCl, 1 mM Mg(OAc)2, 1 mM imidazole, 0.01% NP40, 1 mM TCEP, 0.5 mM EGTA) |
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凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 / デジタル化 - スキャナー: OTHER / 平均電子線量: 4.7 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 77312 |
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初期 角度割当 | タイプ: ANGULAR RECONSTITUTION |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION |
-原子モデル構築 1
精密化 | プロトコル: AB INITIO MODEL |
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得られたモデル | ![]() PDB-5gm6: |