+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 9c4b | |||||||||||||||
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タイトル | Second BAF53a of the human TIP60 complex | |||||||||||||||
要素 | Actin-like protein 6A | |||||||||||||||
キーワード | GENE REGULATION / Chromatin Modification | |||||||||||||||
機能・相同性 | 機能・相同性情報 regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / npBAF complex / brahma complex / GBAF complex / regulation of G0 to G1 transition / neural retina development / regulation of double-strand break repair / regulation of nucleotide-excision repair / Ino80 complex ...regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / npBAF complex / brahma complex / GBAF complex / regulation of G0 to G1 transition / neural retina development / regulation of double-strand break repair / regulation of nucleotide-excision repair / Ino80 complex / RSC-type complex / blastocyst formation / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / spinal cord development / regulation of chromosome organization / positive regulation of stem cell population maintenance / 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 / regulation of embryonic development / negative regulation of cell differentiation / positive regulation of double-strand break repair via homologous recombination / positive regulation of myoblast differentiation / regulation of DNA repair / telomere maintenance / positive regulation of DNA repair / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of cell differentiation / DNA Damage Recognition in GG-NER / kinetochore / RMTs methylate histone arginines / nuclear matrix / UCH proteinases / nucleosome / nervous system development / HATs acetylate histones / regulation of apoptotic process / DNA recombination / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / DNA repair / positive regulation of cell population proliferation / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / signal transduction / protein-containing complex / nucleoplasm / nucleus / plasma membrane 類似検索 - 分子機能 | |||||||||||||||
生物種 | Homo sapiens (ヒト) | |||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | |||||||||||||||
データ登録者 | Yang, Z. / Mameri, A. / Florez Ariza, A.J. / Cote, J. / Nogales, E. | |||||||||||||||
資金援助 | 米国, カナダ, 4件
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引用 | ジャーナル: Science / 年: 2024 タイトル: Structural insights into the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex. 著者: Zhenlin Yang / Amel Mameri / Claudia Cattoglio / Catherine Lachance / Alfredo Jose Florez Ariza / Jie Luo / Jonathan Humbert / Deepthi Sudarshan / Arul Banerjea / Maxime Galloy / Amélie ...著者: Zhenlin Yang / Amel Mameri / Claudia Cattoglio / Catherine Lachance / Alfredo Jose Florez Ariza / Jie Luo / Jonathan Humbert / Deepthi Sudarshan / Arul Banerjea / Maxime Galloy / Amélie Fradet-Turcotte / Jean-Philippe Lambert / Jeff A Ranish / Jacques Côté / Eva Nogales / 要旨: The human nucleosome acetyltransferase of histone H4 (NuA4)/Tat-interactive protein, 60 kilodalton (TIP60) coactivator complex, a fusion of the yeast switch/sucrose nonfermentable related 1 (SWR1) ...The human nucleosome acetyltransferase of histone H4 (NuA4)/Tat-interactive protein, 60 kilodalton (TIP60) coactivator complex, a fusion of the yeast switch/sucrose nonfermentable related 1 (SWR1) and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4, H2A, and H2A.Z to regulate gene expression and maintain genome stability. Our cryo-electron microscopy studies show that, within the NuA4/TIP60 complex, the E1A binding protein P400 (EP400) subunit serves as a scaffold holding the different functional modules in specific positions, creating a distinct arrangement of the actin-related protein (ARP) module. EP400 interacts with the transformation/transcription domain-associated protein (TRRAP) subunit by using a footprint that overlaps with that of the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex, preventing the formation of a hybrid complex. Loss of the TRRAP subunit leads to mislocalization of NuA4/TIP60, resulting in the redistribution of H2A.Z and its acetylation across the genome, emphasizing the dual functionality of NuA4/TIP60 as a single macromolecular assembly. | |||||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 9c4b.cif.gz | 153.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb9c4b.ent.gz | 123.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 9c4b.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 9c4b_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 9c4b_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | 9c4b_validation.xml.gz | 26.5 KB | 表示 | |
CIF形式データ | 9c4b_validation.cif.gz | 35.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/c4/9c4b ftp://data.pdbj.org/pub/pdb/validation_reports/c4/9c4b | HTTPS FTP |
-関連構造データ
関連構造データ | 45180MC 9c47C 9c57C 9c62C 9c6nC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 47509.812 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ACTL6A, BAF53, BAF53A, INO80K / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O96019 |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Second BAF53a of the human TIP60 complex / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: SPOT SCAN |
電子レンズ | モード: 4D-STEM / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
EMソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / カテゴリ: モデル精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 96931 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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