+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0974 | |||||||||
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タイトル | Structure of nucleosome-bound human BAF complex | |||||||||
マップデータ | Structure of nucleosome-bound human BAF complex in the apo state | |||||||||
試料 |
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キーワード | Chromatin remodeler / Complex / GENE REGULATION | |||||||||
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 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport ...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 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport / blastocyst hatching / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / protein localization to adherens junction / brahma complex / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / dense body / Formation of annular gap junctions / regulation of G0 to G1 transition / neural retina development / Gap junction degradation / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / hepatocyte differentiation / regulation of double-strand break repair / adherens junction assembly / regulation of nucleotide-excision repair / Ino80 complex / XY body / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / blastocyst formation / RNA polymerase I preinitiation complex assembly / RHOF GTPase cycle / Regulation of MITF-M-dependent genes involved in pigmentation / N-acetyltransferase activity / Adherens junctions interactions / tight junction / positive regulation by host of viral transcription / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / 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 / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / cellular response to fatty acid / nuclear androgen receptor binding / establishment or maintenance of cell polarity / nuclear chromosome / regulation of cyclin-dependent protein serine/threonine kinase activity / spinal cord development / maintenance of blood-brain barrier / cortical cytoskeleton / regulation of chromosome organization / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of DNA replication / androgen receptor signaling pathway / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / regulation of embryonic development / positive regulation of Wnt signaling pathway / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / positive regulation of DNA repair / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / estrogen receptor signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / neurogenesis / Chromatin modifying enzymes / regulation of DNA repair / DNA polymerase binding / transcription coregulator activity / lysine-acetylated histone binding 類似検索 - 分子機能 | |||||||||
生物種 | Xenopus calcaratus (カエル) / Homo sapiens (ヒト) / Xenopus laevis (アフリカツメガエル) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.7 Å | |||||||||
データ登録者 | Shuang H / Zihan W | |||||||||
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_0974.map.gz | 475.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0974-v30.xml emd-0974.xml | 35.8 KB 35.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0974.png | 8 KB | ||
Filedesc metadata | emd-0974.cif.gz | 11.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0974 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0974 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_0974_validation.pdf.gz | 662.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0974_full_validation.pdf.gz | 662.1 KB | 表示 | |
XML形式データ | emd_0974_validation.xml.gz | 7.9 KB | 表示 | |
CIF形式データ | emd_0974_validation.cif.gz | 9.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0974 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0974 | 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_0974.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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注釈 | Structure of nucleosome-bound human BAF complex in the apo state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 complex
+超分子 #1: Structure of nucleosome-bound human BAF complex
+超分子 #2: Nucleosome
+超分子 #3: BAF
+分子 #1: Histone H3.3
+分子 #2: Histone H4
+分子 #3: Histone H2A type 1
+分子 #4: Histone H2B
+分子 #5: Transcription activator BRG1
+分子 #6: Actin-like protein 6A
+分子 #7: Actin, cytoplasmic 1
+分子 #8: AT-rich interactive domain-containing protein 1A
+分子 #9: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
+分子 #10: SWI/SNF complex subunit SMARCC2
+分子 #11: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
+分子 #12: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
+分子 #13: Zinc finger protein ubi-d4
+分子 #14: DNA (119-MER)
+分子 #15: DNA (119-MER)
+分子 #16: ZINC 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
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 / 前処理 - 時間: 60 sec. |
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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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 / 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: OTHER |
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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: 3.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 3.0.8) / 使用した粒子像数: 320658 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |