+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16452 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Human spliceosomal PM5 C* complex | |||||||||
マップデータ | map of the human spliceosomal PM5 C* complex | |||||||||
試料 |
| |||||||||
キーワード | spliceosome (スプライセオソーム) / nucleus (細胞核) / splicing | |||||||||
機能・相同性 | 機能・相同性情報 regulation of homologous chromosome segregation / endoplasmic reticulum membrane organization / second spliceosomal transesterification activity / exon-exon junction subcomplex mago-y14 / post-spliceosomal complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / spliceosomal complex disassembly / cellular response to selenite ion / negative regulation of nitric-oxide synthase activity ...regulation of homologous chromosome segregation / endoplasmic reticulum membrane organization / second spliceosomal transesterification activity / exon-exon junction subcomplex mago-y14 / post-spliceosomal complex / negative regulation of selenocysteine incorporation / regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / spliceosomal complex disassembly / cellular response to selenite ion / negative regulation of nitric-oxide synthase activity / selenocysteine insertion sequence binding / exon-exon junction complex / NOSIP mediated eNOS trafficking / pre-mRNA 3'-splice site binding / granulocyte differentiation / snRNP binding / post-mRNA release spliceosomal complex / U2 snRNP binding / regulation of retinoic acid receptor signaling pathway / negative regulation of toll-like receptor signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding / regulation of translation at postsynapse, modulating synaptic transmission / 3'-5' RNA helicase activity / U7 snRNP / generation of catalytic spliceosome for first transesterification step / renal system process / negative regulation of excitatory postsynaptic potential / histone pre-mRNA 3'end processing complex / alternative mRNA splicing, via spliceosome / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cis assembly of pre-catalytic spliceosome / regulation of vitamin D receptor signaling pathway / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / negative regulation of catalytic activity / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / negative regulation of interleukin-8 production / regulation of mRNA processing / negative regulation of lipopolysaccharide-mediated signaling pathway / Deadenylation of mRNA / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / embryonic brain development / negative regulation of phosphorylation / protein methylation / U12-type spliceosomal complex / methylosome / STING mediated induction of host immune responses / 7-methylguanosine cap hypermethylation / negative regulation of interferon-beta production / nuclear retinoic acid receptor binding / U2-type catalytic step 1 spliceosome / U1 snRNP binding / pICln-Sm protein complex / Prp19 complex / RNA splicing, via transesterification reactions / poly(A) binding / positive regulation of androgen receptor activity / M-decay: degradation of maternal mRNAs by maternally stored factors / RNA stem-loop binding / mRNA 3'-end processing / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / pre-mRNA binding / sno(s)RNA-containing ribonucleoprotein complex / ATP-dependent activity, acting on RNA / SMN-Sm protein complex / embryonic cranial skeleton morphogenesis / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / U2-type precatalytic spliceosome / IRF3-mediated induction of type I IFN / positive regulation of mRNA splicing, via spliceosome / telomerase holoenzyme complex / C2H2 zinc finger domain binding / regulation of mRNA splicing, via spliceosome / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / commitment complex / positive regulation by host of viral transcription / U4 snRNP / positive regulation of vitamin D receptor signaling pathway / Transport of Mature mRNA derived from an Intron-Containing Transcript / Notch binding / U2 snRNP / nuclear vitamin D receptor binding / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RNA Polymerase II Transcription Termination / RUNX3 regulates NOTCH signaling / U1 snRNP / positive regulation of alpha-beta T cell differentiation / NOTCH4 Intracellular Domain Regulates Transcription / U2-type prespliceosome / ubiquitin-ubiquitin ligase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / K63-linked polyubiquitin modification-dependent protein binding / WD40-repeat domain binding / NOTCH3 Intracellular Domain Regulates Transcription 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / human (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.8 Å | |||||||||
データ登録者 | Dybkov O / Kastner B / Luehrmann R | |||||||||
資金援助 | ドイツ, 1件
| |||||||||
引用 | ジャーナル: Sci Adv / 年: 2023 タイトル: Regulation of 3' splice site selection after step 1 of splicing by spliceosomal C* proteins. 著者: Olexandr Dybkov / Marco Preußner / Leyla El Ayoubi / Vivi-Yun Feng / Caroline Harnisch / Kilian Merz / Paula Leupold / Peter Yudichev / Dmitry E Agafonov / Cindy L Will / Cyrille Girard / ...著者: Olexandr Dybkov / Marco Preußner / Leyla El Ayoubi / Vivi-Yun Feng / Caroline Harnisch / Kilian Merz / Paula Leupold / Peter Yudichev / Dmitry E Agafonov / Cindy L Will / Cyrille Girard / Christian Dienemann / Henning Urlaub / Berthold Kastner / Florian Heyd / Reinhard Lührmann / 要旨: Alternative precursor messenger RNA splicing is instrumental in expanding the proteome of higher eukaryotes, and changes in 3' splice site (3'ss) usage contribute to human disease. We demonstrate by ...Alternative precursor messenger RNA splicing is instrumental in expanding the proteome of higher eukaryotes, and changes in 3' splice site (3'ss) usage contribute to human disease. We demonstrate by small interfering RNA-mediated knockdowns, followed by RNA sequencing, that many proteins first recruited to human C* spliceosomes, which catalyze step 2 of splicing, regulate alternative splicing, including the selection of alternatively spliced NAGNAG 3'ss. Cryo-electron microscopy and protein cross-linking reveal the molecular architecture of these proteins in C* spliceosomes, providing mechanistic and structural insights into how they influence 3'ss usage. They further elucidate the path of the 3' region of the intron, allowing a structure-based model for how the C* spliceosome potentially scans for the proximal 3'ss. By combining biochemical and structural approaches with genome-wide functional analyses, our studies reveal widespread regulation of alternative 3'ss usage after step 1 of splicing and the likely mechanisms whereby C* proteins influence NAGNAG 3'ss choices. | |||||||||
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_16452.map.gz | 373.6 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-16452-v30.xml emd-16452.xml | 92.1 KB 92.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_16452_fsc.xml | 20.1 KB | 表示 | FSCデータファイル |
画像 | emd_16452.png | 117.9 KB | ||
その他 | emd_16452_additional_1.map.gz emd_16452_half_map_1.map.gz emd_16452_half_map_2.map.gz | 30.2 MB 690.5 MB 690.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16452 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16452 | HTTPS FTP |
-関連構造データ
関連構造データ | 8c6jMC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
---|---|
類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_16452.map.gz / 形式: CCP4 / 大きさ: 744.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | map of the human spliceosomal PM5 C* complex | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-追加マップ: locally filtered map of the human spliceosomal PM5 C* complex
ファイル | emd_16452_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | locally filtered map of the human spliceosomal PM5 C* complex | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: half map A
ファイル | emd_16452_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | half map A | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: half map B
ファイル | emd_16452_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | half map B | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : human spliceosomal C* complex assembled on PM5 pre-mRNA
+超分子 #1: human spliceosomal C* complex assembled on PM5 pre-mRNA
+分子 #1: U2 snRNA
+分子 #3: U5 snRNA
+分子 #4: U6 snRNA
+分子 #19: PM5 5' Exon
+分子 #23: PM5 Intron
+分子 #2: Splicing factor ESS-2 homolog
+分子 #5: Eukaryotic initiation factor 4A-III
+分子 #6: RNA-binding protein 8A
+分子 #7: Protein mago nashi homolog
+分子 #8: Pre-mRNA-processing-splicing factor 8
+分子 #9: U5 small nuclear ribonucleoprotein 200 kDa helicase
+分子 #10: 116 kDa U5 small nuclear ribonucleoprotein component
+分子 #11: Peptidyl-prolyl cis-trans isomerase-like 3
+分子 #12: Probable ATP-dependent RNA helicase DDX41
+分子 #13: Peptidyl-prolyl cis-trans isomerase E
+分子 #14: Protein FAM50A
+分子 #15: Pre-mRNA-splicing factor ISY1 homolog
+分子 #16: Nitric oxide synthase-interacting protein
+分子 #17: Splicing factor C9orf78
+分子 #18: PRKR-interacting protein 1
+分子 #20: Splicing factor Cactin
+分子 #21: Protein FAM32A
+分子 #22: Pre-mRNA-splicing factor CWC22 homolog
+分子 #24: Pleiotropic regulator 1
+分子 #25: SNW domain-containing protein 1
+分子 #26: Protein BUD31 homolog
+分子 #27: Pre-mRNA-splicing factor RBM22
+分子 #28: U5 small nuclear ribonucleoprotein 40 kDa protein
+分子 #29: Cell division cycle 5-like protein
+分子 #30: Spliceosome-associated protein CWC15 homolog
+分子 #31: Serine/arginine repetitive matrix protein 2
+分子 #32: Crooked neck-like protein 1
+分子 #33: Pre-mRNA-splicing factor SYF1
+分子 #34: Intron-binding protein aquarius
+分子 #35: ATP-dependent RNA helicase DHX8
+分子 #36: U2 small nuclear ribonucleoprotein A'
+分子 #37: U2 small nuclear ribonucleoprotein B''
+分子 #38: NF-kappa-B-activating protein
+分子 #39: Small nuclear ribonucleoprotein Sm D2
+分子 #40: Small nuclear ribonucleoprotein-associated proteins B and B'
+分子 #41: Small nuclear ribonucleoprotein Sm D1
+分子 #42: Small nuclear ribonucleoprotein Sm D3
+分子 #43: Small nuclear ribonucleoprotein E
+分子 #44: Small nuclear ribonucleoprotein F
+分子 #45: Small nuclear ribonucleoprotein G
+分子 #46: Pre-mRNA-splicing factor SLU7
+分子 #47: Peptidyl-prolyl cis-trans isomerase-like 1
+分子 #48: STING ER exit protein
+分子 #49: Pre-mRNA-processing factor 17
+分子 #50: Pre-mRNA-splicing factor SPF27
+分子 #51: Pre-mRNA-processing factor 19
+分子 #52: Pre-mRNA-splicing factor SYF2
+分子 #53: Splicing regulator SDE2
+分子 #54: POTASSIUM ION
+分子 #55: MAGNESIUM ION
+分子 #56: ADENOSINE-5'-TRIPHOSPHATE
+分子 #57: INOSITOL HEXAKISPHOSPHATE
+分子 #58: GUANOSINE-5'-TRIPHOSPHATE
+分子 #59: 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
濃度 | 0.8 mg/mL |
---|---|
緩衝液 | pH: 7.8 |
グリッド | モデル: Quantifoil R2/2 / 材質: GOLD / メッシュ: 200 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 100 sec. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV |
詳細 | 4 microliter sample was applied to a grid. After 15 s, the grid was blotted for 3 s with a blot force of 5 and vitrified by plunging into liquid ethane using FEI Vitrobot Mark IV. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 81000 |
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 |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 1 / 実像数: 14388 / 平均露光時間: 1.465 sec. / 平均電子線量: 44.24 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
-原子モデル構築 1
初期モデル |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT | ||||||||||||||||||||||||
得られたモデル | PDB-8c6j: |