[日本語] English
万見- EMDB-33424: RNA polymerase II elongation complex transcribing a nucleosome (EC42) -
+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-33424 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | RNA polymerase II elongation complex transcribing a nucleosome (EC42) | ||||||||||||||||||||||||
マップデータ | |||||||||||||||||||||||||
試料 |
| ||||||||||||||||||||||||
キーワード | chromatin / nucleosome / TRANSCRIPTION | ||||||||||||||||||||||||
機能・相同性 | 機能・相同性情報 RNA polymerase II C-terminal domain phosphoserine binding / regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / Cdc73/Paf1 complex / DSIF complex / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / nucleosome organization / muscle cell differentiation ...RNA polymerase II C-terminal domain phosphoserine binding / regulation of septum digestion after cytokinesis / siRNA-mediated pericentric heterochromatin formation / Cdc73/Paf1 complex / DSIF complex / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / nucleosome organization / muscle cell differentiation / regulation of transcription elongation by RNA polymerase II / transcription elongation factor activity / pericentric heterochromatin formation / RPB4-RPB7 complex / inner kinetochore / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / oocyte maturation / transcription elongation-coupled chromatin remodeling / poly(A)+ mRNA export from nucleus / termination of RNA polymerase II transcription / termination of RNA polymerase III transcription / nucleus organization / : / : / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / chromosome, centromeric region / spermatid development / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / single fertilization / transcription elongation by RNA polymerase I / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / protein localization to CENP-A containing chromatin / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / pericentric heterochromatin / translation elongation factor activity / tRNA transcription by RNA polymerase III / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / RNA polymerase I activity / heterochromatin organization / Packaging Of Telomere Ends / RNA polymerase II activity / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / nucleosome binding / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / translation initiation factor binding / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / embryo implantation / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / transcription elongation factor complex / PRC2 methylates histones and DNA / innate immune response in mucosa / regulation of DNA-templated transcription elongation / Defective pyroptosis / HDACs deacetylate histones / transcription elongation by RNA polymerase II / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / P-body / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / ribonucleoside binding 類似検索 - 分子機能 | ||||||||||||||||||||||||
生物種 | Komagataella phaffii (菌類) / Homo sapiens (ヒト) / synthetic construct (人工物) | ||||||||||||||||||||||||
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 | Ehara H / Kujirai T / Shirouzu M / Kurumizaka H / Sekine S | ||||||||||||||||||||||||
資金援助 | 日本, 7件
| ||||||||||||||||||||||||
引用 | ジャーナル: Science / 年: 2022 タイトル: Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT. 著者: Haruhiko Ehara / Tomoya Kujirai / Mikako Shirouzu / Hitoshi Kurumizaka / Shun-Ichi Sekine / 要旨: During gene transcription, RNA polymerase II (RNAPII) traverses nucleosomes in chromatin, but the mechanism has remained elusive. Using cryo-electron microscopy, we obtained structures of the RNAPII ...During gene transcription, RNA polymerase II (RNAPII) traverses nucleosomes in chromatin, but the mechanism has remained elusive. Using cryo-electron microscopy, we obtained structures of the RNAPII elongation complex (EC) passing through a nucleosome in the presence of the transcription elongation factors Spt6, Spn1, Elf1, Spt4/5, and Paf1C and the histone chaperone FACT (facilitates chromatin transcription). The structures show snapshots of EC progression on DNA mediating downstream nucleosome disassembly, followed by its reassembly upstream of the EC, which is facilitated by FACT. FACT dynamically adapts to successively occurring subnucleosome intermediates, forming an interface with the EC. Spt6, Spt4/5, and Paf1C form a "cradle" at the EC DNA-exit site and support the upstream nucleosome reassembly. These structures explain the mechanism by which the EC traverses nucleosomes while maintaining the chromatin structure and epigenetic information. | ||||||||||||||||||||||||
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_33424.map.gz | 40.8 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-33424-v30.xml emd-33424.xml | 63.5 KB 63.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_33424_fsc.xml | 8.5 KB | 表示 | FSCデータファイル |
画像 | emd_33424.png | 109.8 KB | ||
Filedesc metadata | emd-33424.cif.gz | 15.2 KB | ||
その他 | emd_33424_additional_1.map.gz emd_33424_additional_2.map.gz emd_33424_half_map_1.map.gz emd_33424_half_map_2.map.gz | 40.8 MB 40.4 MB 40.9 MB 40.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-33424 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33424 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_33424_validation.pdf.gz | 937 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_33424_full_validation.pdf.gz | 936.9 KB | 表示 | |
XML形式データ | emd_33424_validation.xml.gz | 14.2 KB | 表示 | |
CIF形式データ | emd_33424_validation.cif.gz | 20.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33424 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33424 | HTTPS FTP |
-関連構造データ
関連構造データ | 7xseMC 7xn7C 7xsxC 7xszC 7xt7C 7xtdC 7xtiC 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_33424.map.gz / 形式: CCP4 / 大きさ: 52.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ボクセルのサイズ | X=Y=Z: 1.484 Å | ||||||||||||||||||||
密度 |
| ||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-追加マップ: EC reconstruction
ファイル | emd_33424_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | EC reconstruction | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-追加マップ: nucleosome reconstruction
ファイル | emd_33424_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | nucleosome reconstruction | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_33424_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_33424_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt...
+超分子 #1: RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt...
+超分子 #2: RNA polymerase II
+超分子 #3: Elf1,Spt4/5,Spn1 and Paf1C
+超分子 #4: DNA,RNA
+超分子 #5: histone
+超分子 #6: Spt6
+分子 #1: DNA-directed RNA polymerase subunit
+分子 #2: DNA-directed RNA polymerase subunit beta
+分子 #3: RNA polymerase II third largest subunit B44, part of central core
+分子 #4: RNA polymerase II subunit B32
+分子 #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+分子 #6: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
+分子 #7: RNA polymerase II subunit
+分子 #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #9: DNA-directed RNA polymerase subunit
+分子 #10: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, I...
+分子 #11: RNA polymerase II subunit B12.5
+分子 #12: RNA polymerase subunit ABC10-alpha
+分子 #13: Transcription elongation factor 1 homolog
+分子 #17: Transcription elongation factor SPT4
+分子 #18: Transcription elongation factor SPT5
+分子 #19: Histone H3.3
+分子 #20: Histone H4
+分子 #21: Histone H2A type 1-B/E
+分子 #22: Histone H2B type 1-J
+分子 #23: Transcription elongation factor Spt6
+分子 #24: Protein that interacts with Spt6p and copurifies with Spt5p and R...
+分子 #25: Component of the Paf1p complex
+分子 #26: RNAPII-associated chromatin remodeling Paf1 complex subunit
+分子 #27: Leo1
+分子 #28: RNAP II-associated protein
+分子 #29: Constituent of Paf1 complex with RNA polymerase II, Paf1p, Hpr1p,...
+分子 #14: DNA (198-MER)
+分子 #16: DNA (198-MER)
+分子 #15: RNA (5'-R(P*UP*GP*CP*CP*UP*GP*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*UP*GP...
+分子 #30: ZINC ION
+分子 #31: MAGNESIUM 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: 7.5 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | TFS KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 51.0 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): 2.5 µm / 最小 デフォーカス(公称値): 1.0 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |