+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0968 | |||||||||
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タイトル | Structure of human BAF Base module | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / H3K9me3 modified histone binding / nuclear receptor-mediated glucocorticoid signaling pathway / blastocyst hatching / bBAF complex / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I ...negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / H3K9me3 modified histone binding / nuclear receptor-mediated glucocorticoid signaling pathway / blastocyst hatching / bBAF complex / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / brahma complex / Tat protein binding / GBAF complex / regulation of G0 to G1 transition / neural retina development / EGR2 and SOX10-mediated initiation of Schwann cell myelination / hepatocyte differentiation / regulation of nucleotide-excision repair / XY body / RSC-type complex / RNA polymerase I preinitiation complex assembly / Regulation of MITF-M-dependent genes involved in pigmentation / N-acetyltransferase activity / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / germ cell nucleus / positive regulation of double-strand break repair / positive regulation of T cell differentiation / cellular response to fatty acid / nuclear androgen receptor binding / nuclear chromosome / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / androgen receptor signaling pathway / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / estrogen receptor signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / neurogenesis / Chromatin modifying enzymes / DNA polymerase binding / transcription coregulator activity / lysine-acetylated histone binding / transcription coregulator binding / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / positive regulation of miRNA transcription / helicase activity / nuclear receptor binding / positive regulation of cell differentiation / apoptotic signaling pathway / Formation of the beta-catenin:TCF transactivating complex / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / positive regulation of DNA-binding transcription factor activity / negative regulation of cell growth / p53 binding / RMTs methylate histone arginines / kinetochore / fibrillar center / nuclear matrix / DNA integration / transcription corepressor activity / nervous system development / positive regulation of cold-induced thermogenesis / histone binding / transcription coactivator activity / molecular adaptor activity / chromatin remodeling / hydrolase activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / centrosome / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / nucleolus / apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular space / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytosol 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: 3.0 Å | |||||||||
データ登録者 | Shuang H / Zihan W / Yuan T / Zishuo Y / Jiali Y / Xinxin W / Jie L / Bijun L / Yanhui X | |||||||||
引用 | ジャーナル: Science / 年: 2020 タイトル: Structure of nucleosome-bound human BAF complex. 著者: Shuang He / Zihan Wu / Yuan Tian / Zishuo Yu / Jiali Yu / Xinxin Wang / Jie Li / Bijun Liu / Yanhui Xu / 要旨: Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to ...Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to cancers. The 3.7-angstrom-resolution cryo-electron microscopy structure of human BAF bound to the nucleosome reveals that the nucleosome is sandwiched by the base and the adenosine triphosphatase (ATPase) modules, which are bridged by the actin-related protein (ARP) module. The ATPase motor is positioned proximal to nucleosomal DNA and, upon ATP hydrolysis, engages with and pumps DNA along the nucleosome. The C-terminal α helix of SMARCB1, enriched in positively charged residues frequently mutated in cancers, mediates interactions with an acidic patch of the nucleosome. AT-rich interactive domain-containing protein 1A (ARID1A) and the SWI/SNF complex subunit SMARCC serve as a structural core and scaffold in the base module organization, respectively. Our study provides structural insights into subunit organization and nucleosome recognition of human BAF complex. | |||||||||
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_0968.map.gz | 25.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0968-v30.xml emd-0968.xml | 14.4 KB 14.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0968.png | 5.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0968 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0968 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0968_validation.pdf.gz | 291 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0968_full_validation.pdf.gz | 290.6 KB | 表示 | |
XML形式データ | emd_0968_validation.xml.gz | 8 KB | 表示 | |
CIF形式データ | emd_0968_validation.cif.gz | 9.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0968 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0968 | 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_0968.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.04 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
-試料の構成要素
-全体 : Structure of nucleosome-bound human BAF Base module
全体 | 名称: Structure of nucleosome-bound human BAF Base module |
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要素 |
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-超分子 #1: Structure of nucleosome-bound human BAF Base module
超分子 | 名称: Structure of nucleosome-bound human BAF Base module / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#20 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) / 組換細胞: HEK293T |
-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 |
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / 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: PLASMA CLEANING |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / デジタル化 - 画像ごとのフレーム数: 1-32 / 平均電子線量: 50.0 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: OTHER |
試料ステージ | 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
CTF補正 | ソフトウェア - 名称: Gctf (ver. 1.06) |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: cryoSPARC (ver. 2.12.4) / 使用した粒子像数: 197606 |
初期 角度割当 | タイプ: OTHER / ソフトウェア - 名称: cryoSPARC (ver. 2.12.4) |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.0.8) |
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: AB INITIO MODEL |
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得られたモデル | PDB-6lth: |