+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4692 | |||||||||
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タイトル | Human-D02 Nucleosome Core Particle with biotin-streptavidin label | |||||||||
マップデータ | human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end | |||||||||
試料 |
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キーワード | chromatin (クロマチン) / nucleosome (ヌクレオソーム) / retrovirus (レトロウイルス科) / DNA BINDING PROTEIN (DNA結合タンパク質) | |||||||||
機能・相同性 | 機能・相同性情報 nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / 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 / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNAメチル化 / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / RMTs methylate histone arginines / 遺伝的組換え / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / ヌクレオソーム / antimicrobial humoral immune response mediated by antimicrobial peptide / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / enzyme binding / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / 核質 / 生体膜 / identical protein binding / 細胞核 / 細胞質基質 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.2 Å | |||||||||
データ登録者 | Wilson MD / Nans A / Pye VE / 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_4692.map.gz | 5.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4692-v30.xml emd-4692.xml | 29.8 KB 29.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4692_fsc.xml | 9.2 KB | 表示 | FSCデータファイル |
画像 | emd_4692.png | 56.8 KB | ||
マスクデータ | emd_4692_msk_1.map | 64 MB | マスクマップ | |
Filedesc metadata | emd-4692.cif.gz | 7.6 KB | ||
その他 | emd_4692_additional.map.gz emd_4692_half_map_1.map.gz emd_4692_half_map_2.map.gz | 59.8 MB 49.6 MB 49.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4692 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4692 | 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_4692.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.09 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
-マスク #1
ファイル | emd_4692_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: unmasked map for human nucleosome core particle wrapped...
ファイル | emd_4692_additional.map | ||||||||||||
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注釈 | unmasked map for human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end | ||||||||||||
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 for human nucleosome core particle...
ファイル | emd_4692_half_map_1.map | ||||||||||||
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注釈 | half map 1 for human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end | ||||||||||||
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 for human nucleosome core particle...
ファイル | emd_4692_half_map_2.map | ||||||||||||
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注釈 | half map 1 for human nucleosome core particle wrapped with 145bp of D02 DNA with biotin-streptavidin at distal end | ||||||||||||
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 : Human-D02 Nucleosome Core Particle with biotin-streptavidin label
+超分子 #1: Human-D02 Nucleosome Core Particle with biotin-streptavidin label
+超分子 #2: Histones
+超分子 #3: 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: DNA (142-MER)
+分子 #6: DNA (142-MER)
+分子 #7: MANGANESE (II) 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 | 0.176 mg/mL | |||||||||||||||
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緩衝液 | pH: 7 構成要素:
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グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / メッシュ: 300 / 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: GLOW DISCHARGE / 前処理 - 時間: 60 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 K / 装置: FEI VITROBOT MARK IV | |||||||||||||||
詳細 | Streptavidin incubated D02-biotin nucleosomes were crosslinked with glutaraldehye. This was quenched and the sample spin concentrated |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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): 0.0035 µm / 最小 デフォーカス(公称値): 0.0015 µm / 倍率(公称値): 75000 |
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: FEI FALCON III (4k x 4k) 検出モード: COUNTING / 撮影したグリッド数: 1 / 実像数: 4182 / 平均露光時間: 60.0 sec. / 平均電子線量: 28.3 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 | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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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. 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-6r0c: |