+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-32074 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | The cryo-EM structure of the human pre-A complex | |||||||||
マップデータ | The cryo-EM map for the U2 part of human pre-A complex | |||||||||
試料 |
| |||||||||
キーワード | human spliceosome / pre-A complex / PRP5 / A complex / U1 snRNP / U2 snRNP / SPLICING | |||||||||
機能・相同性 | 機能・相同性情報 nuclear body organization / negative regulation of protein refolding / U2AF complex / regulation of steroid biosynthetic process / regulation of ATP-dependent activity / U11/U12 snRNP / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP ...nuclear body organization / negative regulation of protein refolding / U2AF complex / regulation of steroid biosynthetic process / regulation of ATP-dependent activity / U11/U12 snRNP / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / histone pre-mRNA 3'end processing complex / Leydig cell differentiation / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / male sex determination / splicing factor binding / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / P granule / SMN-Sm protein complex / regulation of mRNA splicing, via spliceosome / spliceosomal tri-snRNP complex / negative regulation of chaperone-mediated autophagy / telomerase holoenzyme complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / U2-type precatalytic spliceosome / commitment complex / telomerase RNA binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / SAGA complex / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / pre-mRNA 5'-splice site binding / U2-type prespliceosome / intercellular bridge / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / regulation of alternative mRNA splicing, via spliceosome / mRNA 5'-splice site recognition / regulation of RNA splicing / mRNA 3'-splice site recognition / U5 snRNP / U2 snRNA binding / regulation of DNA repair / spliceosomal snRNP assembly / Cajal body / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / Hsp70 protein binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / stem cell differentiation / negative regulation of smooth muscle cell proliferation / spliceosomal complex / B-WICH complex positively regulates rRNA expression / negative regulation of protein catabolic process / fibrillar center / mRNA processing / cytoplasmic ribonucleoprotein granule / nuclear matrix / mRNA splicing, via spliceosome / positive regulation of neuron projection development / transcription corepressor activity / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / spermatogenesis / RNA helicase activity / single-stranded RNA binding / nuclear body / ribosome / RNA helicase / nuclear speck / chromatin remodeling / mRNA binding / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / enzyme binding / protein homodimerization activity / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / unidentified adenovirus (ウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.0 Å | |||||||||
データ登録者 | Zhang X / Zhan X / Shi Y | |||||||||
資金援助 | 中国, 1件
| |||||||||
引用 | ジャーナル: Nat Struct Mol Biol / 年: 2024 タイトル: Structural insights into branch site proofreading by human spliceosome. 著者: Xiaofeng Zhang / Xiechao Zhan / Tong Bian / Fenghua Yang / Pan Li / Yichen Lu / Zhihan Xing / Rongyan Fan / Qiangfeng Cliff Zhang / Yigong Shi / 要旨: Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the ...Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the underlying mechanism remains unclear. Here we report the atomic structures of two sequential complexes leading to prespliceosome assembly: human 17S U2 snRNP and a cross-exon pre-A complex. PRP5 is anchored on 17S U2 snRNP mainly through occupation of the RNA path of SF3B1 by an acidic loop of PRP5; the helicase domain of PRP5 associates with U2 snRNA; the BS-interacting stem-loop (BSL) of U2 snRNA is shielded by TAT-SF1, unable to engage the BS. In the pre-A complex, an initial U2-BS duplex is formed; the translocated helicase domain of PRP5 stays with U2 snRNA and the acidic loop still occupies the RNA path. The pre-A conformation is specifically stabilized by the splicing factors SF1, DNAJC8 and SF3A2. Cancer-derived mutations in SF3B1 damage its association with PRP5, compromising BS proofreading. Together, these findings reveal key insights into prespliceosome assembly and BS selection or proofreading by PRP5. | |||||||||
履歴 |
|
-構造の表示
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_32074.map.gz | 398.8 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-32074-v30.xml emd-32074.xml | 47.3 KB 47.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_32074.png | 64.2 KB | ||
Filedesc metadata | emd-32074.cif.gz | 13.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-32074 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32074 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_32074_validation.pdf.gz | 468.1 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_32074_full_validation.pdf.gz | 467.7 KB | 表示 | |
XML形式データ | emd_32074_validation.xml.gz | 7.6 KB | 表示 | |
CIF形式データ | emd_32074_validation.cif.gz | 8.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32074 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32074 | 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_32074.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | The cryo-EM map for the U2 part of human pre-A complex | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.087 Å | ||||||||||||||||||||
密度 |
| ||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-試料の構成要素
+全体 : human pre-A complex
+超分子 #1: human pre-A complex
+超分子 #2: human pre-A
+超分子 #3: pre-mRNA, 5SS
+分子 #1: Splicing factor 3A subunit 2
+分子 #2: Splicing factor 1
+分子 #3: DnaJ homolog subfamily C member 8
+分子 #5: Splicing factor 3B subunit 1
+分子 #6: Splicing factor 3B subunit 2
+分子 #7: Splicing factor 3B subunit 3
+分子 #8: Splicing factor 3B subunit 4
+分子 #9: Splicing factor 3B subunit 5
+分子 #10: Splicing factor 3A subunit 1
+分子 #11: Splicing factor 3A subunit 3
+分子 #12: Probable ATP-dependent RNA helicase DDX46
+分子 #13: U2 small nuclear ribonucleoprotein A'
+分子 #14: U2 small nuclear ribonucleoprotein B''
+分子 #15: Small nuclear ribonucleoprotein Sm D2
+分子 #16: Small nuclear ribonucleoprotein F
+分子 #17: Small nuclear ribonucleoprotein E
+分子 #18: Small nuclear ribonucleoprotein G
+分子 #19: Small nuclear ribonucleoprotein Sm D3
+分子 #20: Small nuclear ribonucleoprotein-associated proteins B and B'
+分子 #21: Small nuclear ribonucleoprotein Sm D1
+分子 #25: U1 small nuclear ribonucleoprotein 70 kDa
+分子 #26: U1 small nuclear ribonucleoprotein A
+分子 #27: U1 small nuclear ribonucleoprotein C
+分子 #28: PHD finger-like domain-containing protein 5A
+分子 #4: U2 snRNA
+分子 #22: pre-mRNA
+分子 #23: 5SS
+分子 #24: U1 snRNA
+分子 #29: ZINC ION
+分子 #30: spliceostatin A (form II)
-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 K3 (6k 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 / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 1.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: INSILICO MODEL |
---|---|
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 419522 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |