+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4960 | |||||||||
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タイトル | PFV intasome - nucleosome strand transfer complex | |||||||||
マップデータ | Nucleosome core particle bound by PFV intasome post catalytic state | |||||||||
試料 |
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キーワード | chromatin / nucleosome / retrovirus / DNA BINDING PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / ribonuclease H / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; アスパラギン酸プロテアーゼ / nucleus organization ...negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / ribonuclease H / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; アスパラギン酸プロテアーゼ / nucleus organization / spermatid development / single fertilization / subtelomeric heterochromatin formation / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / 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 / Inhibition of DNA recombination at telomere / telomere organization / embryo implantation / Meiotic synapsis / RNA Polymerase I Promoter Opening / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / virion component / Formation of the beta-catenin:TCF transactivating complex / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / multicellular organism growth / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Metalloprotease DUBs / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / DNA integration / viral genome integration into host DNA / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA-directed DNA polymerase / establishment of integrated proviral latency / HCMV Early Events / viral penetration into host nucleus / osteoblast differentiation / Transcriptional regulation of granulopoiesis / male gonad development / structural constituent of chromatin / RNA-directed DNA polymerase activity / UCH proteinases / RNA-DNA hybrid ribonuclease activity / antimicrobial humoral immune response mediated by antimicrobial peptide / 転移酵素; リンを含む基を移すもの; 核酸を移すもの / nucleosome / host cell / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / antibacterial humoral response / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / DNA recombination / Estrogen-dependent gene expression / host cell cytoplasm / cell population proliferation / chromosome, telomeric region / DNA-directed DNA polymerase 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Human spumaretrovirus (ウイルス) / Pyrobaculum filamentous virus 1 (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: 3.9 Å | |||||||||
データ登録者 | Renault L / Maskell DP / Wilson MD / Cherepanov P / Costa A | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Nat Commun / 年: 2019 タイトル: Retroviral integration into nucleosomes through DNA looping and sliding along the histone octamer. 著者: Marcus D Wilson / Ludovic Renault / Daniel P Maskell / Mohamed Ghoneim / Valerie E Pye / Andrea Nans / David S Rueda / Peter Cherepanov / Alessandro Costa / 要旨: Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase ...Retroviral integrase can efficiently utilise nucleosomes for insertion of the reverse-transcribed viral DNA. In face of the structural constraints imposed by the nucleosomal structure, integrase gains access to the scissile phosphodiester bonds by lifting DNA off the histone octamer at the site of integration. To clarify the mechanism of DNA looping by integrase, we determined a 3.9 Å resolution structure of the prototype foamy virus intasome engaged with a nucleosome core particle. The structural data along with complementary single-molecule Förster resonance energy transfer measurements reveal twisting and sliding of the nucleosomal DNA arm proximal to the integration site. Sliding the nucleosomal DNA by approximately two base pairs along the histone octamer accommodates the necessary DNA lifting from the histone H2A-H2B subunits to allow engagement with the intasome. Thus, retroviral integration into nucleosomes involves the looping-and-sliding mechanism for nucleosomal DNA repositioning, bearing unexpected similarities to chromatin remodelers. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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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_4960.map.gz | 4.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4960-v30.xml emd-4960.xml | 34.2 KB 34.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4960_fsc.xml | 7.7 KB | 表示 | FSCデータファイル |
画像 | emd_4960.png | 281.4 KB | ||
Filedesc metadata | emd-4960.cif.gz | 8.4 KB | ||
その他 | emd_4960_half_map_1.map.gz emd_4960_half_map_2.map.gz | 40.7 MB 40.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4960 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4960 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4960_validation.pdf.gz | 646.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_4960_full_validation.pdf.gz | 646.2 KB | 表示 | |
XML形式データ | emd_4960_validation.xml.gz | 14.6 KB | 表示 | |
CIF形式データ | emd_4960_validation.cif.gz | 19.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4960 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4960 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「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_4960.map.gz / 形式: CCP4 / 大きさ: 52.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Nucleosome core particle bound by PFV intasome post catalytic state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.111 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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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
-ハーフマップ: Half map 1 of Nucleosome core particle bound...
ファイル | emd_4960_half_map_1.map | ||||||||||||
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注釈 | Half map 1 of Nucleosome core particle bound by PFV intasome post catalytic state | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 1 of Nucleosome core particle bound...
ファイル | emd_4960_half_map_2.map | ||||||||||||
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注釈 | Half map 1 of Nucleosome core particle bound by PFV intasome post catalytic state | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Nucleosome core particle bound by PFV intasome post in the post c...
+超分子 #1: Nucleosome core particle bound by PFV intasome post in the post c...
+超分子 #2: Nucleosome
+超分子 #3: Integrase
+超分子 #4: Human DNA
+超分子 #5: DNA
+分子 #1: Histone H3.3
+分子 #2: Histone H4
+分子 #3: Histone H2A type 1
+分子 #4: Histone H2B type 1-C/E/F/G/I
+分子 #5: Integrase
+分子 #6: DNA (128-MER)
+分子 #7: DNA (108-MER)
+分子 #8: DNA (33-MER)
+分子 #9: DNA (53-MER)
+分子 #10: DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*C)-3')
+分子 #11: MAGNESIUM ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.1 mg/mL |
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緩衝液 | pH: 7 / 構成要素 - 濃度: 1.0 MM / 構成要素 - 名称: DTT |
グリッド | モデル: C-flat-1/1 / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: PLASMA CLEANING |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 80 % / チャンバー内温度: 277 K / 装置: LEICA EM CPC / 詳細: 1 min incubation 3.5s blot. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | 球面収差補正装置: Microscope was modified with a Cs corrector (NeCEN netherlands) |
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / 撮影したグリッド数: 2 / 実像数: 4916 / 平均露光時間: 1.6 sec. / 平均電子線量: 56.0 e/Å2 |
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 FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 0.0035 µm / 最小 デフォーカス(公称値): 0.0015 µm / 倍率(公称値): 59000 |
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 |
+画像解析
-原子モデル構築 1
初期モデル |
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詳細 | The initial model was placed in the density using Chimera. Manual building was performed in Coot and final refinement was carried out using phenix.real_space_refine and namdinator. Additional restraints describing protein secondary structure, DNA base pairing and stacking were used in Phenix. | ||||||
精密化 | 空間: REAL | ||||||
得られたモデル | PDB-6rny: |