+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-17252 | ||||||||||||
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タイトル | Structure of TRF1core in complex with telomeric nucleosome | ||||||||||||
マップデータ | Postprocess map of TRF1core-TeloNCP 2:1 complex | ||||||||||||
試料 |
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キーワード | Telomeric nucleosome / shelterin / telomere / DNA BINDING PROTEIN | ||||||||||||
機能・相同性 | 機能・相同性情報 positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / telomerase activity / t-circle formation ...positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / telomerase activity / t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / Telomere C-strand (Lagging Strand) Synthesis / : / positive regulation of telomere maintenance / nuclear telomere cap complex / ankyrin repeat binding / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / telomere capping / DNA binding, bending / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of DNA replication / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / telomere maintenance via telomerase / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / epigenetic regulation of gene expression / 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 / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / telomere maintenance / 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 / PRC2 methylates histones and DNA / innate immune response in mucosa / 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 / 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 / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / fibrillar center / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / spindle / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / nucleosome / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Processing of DNA double-strand break ends / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / microtubule binding 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: 2.7 Å | ||||||||||||
データ登録者 | Hu H / van Roon AMM / Ghanim GE / Ahsan B / Oluwole A / Peak-Chew S / Robinson CV / Nguyen THD | ||||||||||||
資金援助 | 英国, European Union, 米国, 3件
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引用 | ジャーナル: Sci Adv / 年: 2023 タイトル: Structural basis of telomeric nucleosome recognition by shelterin factor TRF1. 著者: Hongmiao Hu / Anne-Marie M van Roon / George E Ghanim / Bilal Ahsan / Abraham O Oluwole / Sew-Yeu Peak-Chew / Carol V Robinson / Thi Hoang Duong Nguyen / 要旨: Shelterin and nucleosomes are the key players that organize mammalian chromosome ends into the protective telomere caps. However, how they interact with each other at telomeres remains unknown. We ...Shelterin and nucleosomes are the key players that organize mammalian chromosome ends into the protective telomere caps. However, how they interact with each other at telomeres remains unknown. We report cryo-electron microscopy structures of a human telomeric nucleosome both unbound and bound to the shelterin factor TRF1. Our structures reveal that TRF1 binds unwrapped nucleosomal DNA ends by engaging both the nucleosomal DNA and the histone octamer. Unexpectedly, TRF1 binding shifts the register of the nucleosomal DNA by 1 bp. We discovered that phosphorylation of the TRF1 C terminus and a noncanomical DNA binding surface on TRF1 are critical for its association with telomeric nucleosomes. These insights into shelterin-chromatin interactions have crucial implications for understanding telomeric chromatin organization and other roles of shelterin at telomeres including replication and transcription. | ||||||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_17252.map.gz | 259.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-17252-v30.xml emd-17252.xml | 33 KB 33 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_17252_fsc.xml | 14.8 KB | 表示 | FSCデータファイル |
画像 | emd_17252.png | 569 KB | ||
その他 | emd_17252_additional_1.map.gz emd_17252_half_map_1.map.gz emd_17252_half_map_2.map.gz | 226.3 MB 227 MB 227 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-17252 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17252 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_17252_validation.pdf.gz | 1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_17252_full_validation.pdf.gz | 1 MB | 表示 | |
XML形式データ | emd_17252_validation.xml.gz | 22.3 KB | 表示 | |
CIF形式データ | emd_17252_validation.cif.gz | 29.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17252 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17252 | 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_17252.map.gz / 形式: CCP4 / 大きさ: 282.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Postprocess map of TRF1core-TeloNCP 2:1 complex | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.826 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: Refine3D map of TRF1core-TeloNCP 2:1 complex
ファイル | emd_17252_additional_1.map | ||||||||||||
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注釈 | Refine3D map of TRF1core-TeloNCP 2:1 complex | ||||||||||||
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 of TRF1core-TeloNCP 2:1 complex
ファイル | emd_17252_half_map_1.map | ||||||||||||
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注釈 | half map of TRF1core-TeloNCP 2:1 complex | ||||||||||||
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 of TRF1core-TeloNCP 2:1 complex
ファイル | emd_17252_half_map_2.map | ||||||||||||
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注釈 | half map of TRF1core-TeloNCP 2:1 complex | ||||||||||||
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 : TRF1core in complex with telomeric nucleosome
+超分子 #1: TRF1core in complex with telomeric nucleosome
+超分子 #2: Human telomeric nucleosome
+超分子 #3: Human TRF1core complex
+分子 #1: Histone H3.1
+分子 #2: Histone H4
+分子 #3: Histone H2A type 1-C
+分子 #4: Histone H2B type 1-C/E/F/G/I
+分子 #7: Telomeric repeat-binding factor 1
+分子 #8: Telomeric repeat-binding factor 1
+分子 #5: Telomeric DNA C strand
+分子 #6: Telomeric DNA G strand
+分子 #9: water
-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
緩衝液 | pH: 8 構成要素:
詳細: 25 mM HEPES-KOH pH 8.0, 150 mM KCl, 1 mM MgCl2, 1% glycerol, 0.01% Igepal CA-630, 1 mM DTT | |||||||||||||||||||||
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グリッド | モデル: C-flat-1.2/1.3 / 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: 70 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: Blot Force: -15 Blot Time: 2.5 s. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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温度 | 最低: 78.0 K |
特殊光学系 | エネルギーフィルター - 名称: GIF Quantum LS / エネルギーフィルター - スリット幅: 20 eV |
ソフトウェア | 名称: EPU (ver. 2.13.0.3175REL) |
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: 24566 / 平均露光時間: 2.25 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: 50.0 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): 2.5 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 105000 |
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
ソフトウェア | 名称: UCSF ChimeraX (ver. 1.5) |
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得られたモデル | PDB-8ox1: |