+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 / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport / morphogenesis of a polarized epithelium ...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 / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / negative regulation of androgen receptor signaling pathway / blastocyst hatching / postsynaptic actin cytoskeleton organization / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / protein localization to adherens junction / postsynaptic actin cytoskeleton / brahma complex / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / regulation of G0 to G1 transition / neural retina development / Formation of annular gap junctions / dense body / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / hepatocyte differentiation / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / RSC-type complex / adherens junction assembly / XY body / Ino80 complex / Prefoldin mediated transfer of substrate to CCT/TriC / RNA polymerase I preinitiation complex assembly / blastocyst formation / RHOF GTPase cycle / 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 mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / positive regulation of double-strand break repair / regulation of norepinephrine uptake / germ cell nucleus / positive regulation of T cell differentiation / regulation of synaptic vesicle endocytosis / apical junction complex / cellular response to fatty acid / establishment or maintenance of cell polarity / nuclear androgen receptor binding / nuclear chromosome / regulation of cyclin-dependent protein serine/threonine kinase activity / cortical cytoskeleton / maintenance of blood-brain barrier / spinal cord development / positive regulation of stem cell population maintenance / regulation of chromosome organization / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of DNA replication / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / brush border / kinesin binding / calyx of Held / regulation of embryonic development / negative regulation of cell differentiation / positive regulation of double-strand break repair via homologous recombination / positive regulation of Wnt signaling pathway / EPH-ephrin mediated repulsion of cells / positive regulation of myoblast differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / regulation of DNA repair / DNA polymerase binding / substantia nigra development / EPHB-mediated forward signaling / positive regulation of DNA repair / telomere maintenance / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / neurogenesis 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.04 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 |