+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 (遺伝子発現の調節) | |||||||||
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 / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / H3K9me3 modified histone binding / positive regulation of norepinephrine uptake / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / intracellular glucocorticoid receptor signaling pathway / cellular response to cytochalasin B ...negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / H3K9me3 modified histone binding / positive regulation of norepinephrine uptake / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / intracellular glucocorticoid receptor signaling pathway / cellular response to cytochalasin B / blastocyst hatching / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / GBAF complex / neural retina development / postsynaptic actin cytoskeleton / protein localization to adherens junction / regulation of G0 to G1 transition / Formation of annular gap junctions / dense body / Tat protein binding / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / EGR2 and SOX10-mediated initiation of Schwann cell myelination / regulation of double-strand break repair / nucleosome disassembly / Ino80 complex / regulation of nucleotide-excision repair / apical protein localization / hepatocyte differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / XY body / blastocyst formation / adherens junction assembly / RHOF GTPase cycle / RSC-type complex / Adherens junctions interactions / RNA polymerase I preinitiation complex assembly / N-acetyltransferase activity / positive regulation by host of viral transcription / 密着結合 / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / ATP-dependent chromatin remodeler activity / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / regulation of norepinephrine uptake / positive regulation of double-strand break repair / germ cell nucleus / positive regulation of T cell differentiation / regulation of synaptic vesicle endocytosis / cellular response to fatty acid / NuA4 histone acetyltransferase complex / nuclear androgen receptor binding / apical junction complex / establishment or maintenance of cell polarity / regulation of chromosome organization / maintenance of blood-brain barrier / spinal cord development / nuclear chromosome / positive regulation of stem cell population maintenance / cortical cytoskeleton / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / nitric-oxide synthase binding / regulation of DNA replication / androgen receptor signaling pathway / regulation of cyclin-dependent protein serine/threonine kinase activity / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / kinesin binding / negative regulation of cell differentiation / regulation of embryonic development / ヘルト萼状シナプス / 刷子縁 / positive regulation of double-strand break repair via homologous recombination / positive regulation of Wnt signaling pathway / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / intracellular estrogen receptor signaling pathway / nucleosomal DNA binding / ATP-dependent activity, acting on DNA / regulation of protein localization to plasma membrane / nucleosome binding / Chromatin modifying enzymes / regulation of DNA repair / DNA polymerase binding / transcription initiation-coupled chromatin remodeling / EPHB-mediated forward signaling 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 |
-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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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 |
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 |
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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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
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 |