+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8x19 | ||||||
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タイトル | Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state | ||||||
要素 |
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キーワード | DNA BINDING PROTEIN/DNA / Remodeler / SRCAP / H2A.Z / DNA BINDING PROTEIN-DNA complex | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of lymphoid progenitor cell differentiation / ATP-dependent H2AZ histone chaperone activity / modification-dependent protein binding / intestinal stem cell homeostasis / promoter-enhancer loop anchoring activity / 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 ...positive regulation of lymphoid progenitor cell differentiation / ATP-dependent H2AZ histone chaperone activity / modification-dependent protein binding / intestinal stem cell homeostasis / promoter-enhancer loop anchoring activity / 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 / histone chaperone activity / establishment of protein localization to chromatin / morphogenesis of a polarized epithelium / bBAF complex / R2TP complex / postsynaptic actin cytoskeleton organization / npBAF complex / protein localization to adherens junction / nBAF complex / postsynaptic actin cytoskeleton / brahma complex / dynein axonemal particle / heart process / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / RPAP3/R2TP/prefoldin-like complex / Swr1 complex / GBAF complex / regulation of G0 to G1 transition / neural retina development / muscle cell differentiation / Formation of annular gap junctions / dense body / Gap junction degradation / Cell-extracellular matrix interactions / positive regulation of telomerase RNA localization to Cajal body / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / Ino80 complex / Activation of the TFAP2 (AP-2) family of transcription factors / RSC-type complex / nucleolus organization / Prefoldin mediated transfer of substrate to CCT/TriC / blastocyst formation / RHOF GTPase cycle / Adherens junctions interactions / tight junction / protein folding chaperone complex / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by outer hair cells of the cochlea / box C/D snoRNP assembly / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / regulation of norepinephrine uptake / positive regulation of double-strand break repair / ATP-dependent chromatin remodeler activity / positive regulation of T cell differentiation / negative regulation of transcription by RNA polymerase I / regulation of synaptic vesicle endocytosis / apical junction complex / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of transcription by RNA polymerase I / cortical cytoskeleton / maintenance of blood-brain barrier / NuA4 histone acetyltransferase complex / spinal cord development / regulation of chromosome organization / positive regulation of stem cell population maintenance / 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 / somatic stem cell population maintenance / Recycling pathway of L1 / brush border / kinesin binding / TFIID-class transcription factor complex binding / regulation of embryonic development / negative regulation of cell differentiation / MLL1 complex / calyx of Held / Telomere Extension By Telomerase / nucleosome binding / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / positive regulation of myoblast differentiation / positive regulation of transcription initiation by RNA polymerase II / regulation of protein localization to plasma membrane / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / protein localization to CENP-A containing chromatin 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: 3.2 Å | ||||||
データ登録者 | Yu, J. / Wang, Q. / Yu, Z. / Li, W. / Wang, L. / Xu, Y. | ||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Cell Discov / 年: 2024 タイトル: Structural insights into histone exchange by human SRCAP complex. 著者: Jiali Yu / Fengrui Sui / Feng Gu / Wanjun Li / Zishuo Yu / Qianmin Wang / Shuang He / Li Wang / Yanhui Xu / 要旨: Histone variant H2A.Z is found at promoters and regulates transcription. The ATP-dependent chromatin remodeler SRCAP complex (SRCAP-C) promotes the replacement of canonical histone H2A-H2B dimer with ...Histone variant H2A.Z is found at promoters and regulates transcription. The ATP-dependent chromatin remodeler SRCAP complex (SRCAP-C) promotes the replacement of canonical histone H2A-H2B dimer with H2A.Z-H2B dimer. Here, we determined structures of human SRCAP-C bound to H2A-containing nucleosome at near-atomic resolution. The SRCAP subunit integrates a 6-subunit actin-related protein (ARP) module and an ATPase-containing motor module. The ATPase-associated ARP module encircles half of the nucleosome along the DNA and may restrain net DNA translocation, a unique feature of SRCAP-C. The motor module adopts distinct nucleosome binding modes in the apo (nucleotide-free), ADP-bound, and ADP-BeF-bound states, suggesting that ATPase-driven movement destabilizes H2A-H2B by unwrapping the entry DNA and pulls H2A-H2B out of nucleosome through the ZNHIT1 subunit. Structure-guided chromatin immunoprecipitation sequencing analysis confirmed the requirement of H2A-contacting ZNHIT1 in maintaining H2A.Z occupancy on the genome. Our study provides structural insights into the mechanism of H2A-H2A.Z exchange mediated by SRCAP-C. | ||||||
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 | 8x19.cif.gz | 1.3 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8x19.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 8x19.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 | 8x19_validation.pdf.gz | 1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8x19_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | 8x19_validation.xml.gz | 148.5 KB | 表示 | |
CIF形式データ | 8x19_validation.cif.gz | 219.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/x1/8x19 ftp://data.pdbj.org/pub/pdb/validation_reports/x1/8x19 | HTTPS FTP |
-関連構造データ
関連構造データ | 37988MC 8x15C 8x1cC 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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-要素
-タンパク質 , 14種, 23分子 AEBFCGDHIJKLMOQNPRSUTVW
#1: タンパク質 | 分子量: 14135.523 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: H2AC6, H2AFL, HIST1H2AC / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q93077 #2: タンパク質 | 分子量: 13937.213 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 遺伝子: H2BC4, H2BFL, HIST1H2BC, H2BC6, H2BFH, HIST1H2BE, H2BC7, H2BFG, HIST1H2BF, H2BC8, H2BFA, HIST1H2BG, H2BC10, H2BFK, HIST1H2BI 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62807 #3: タンパク質 | 分子量: 15437.167 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 遺伝子: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...遺伝子: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P68431 #4: タンパク質 | 分子量: 11394.426 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 遺伝子: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...遺伝子: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62805 #5: タンパク質 | | 分子量: 343915.250 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: SRCAP, KIAA0309 / 発現宿主: Homo sapiens (ヒト) 参照: UniProt: Q6ZRS2, 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 #6: タンパク質 | | 分子量: 40658.363 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: VPS72, TCFL1, YL1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q15906 #7: タンパク質 | | 分子量: 45857.902 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: ACTR6, CDA12 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9GZN1 #8: タンパク質 | | 分子量: 17567.023 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: ZNHIT1, CGBP1, ZNFN4A1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O43257 #9: タンパク質 | 分子量: 50296.914 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RUVBL1, INO80H, NMP238, TIP49, TIP49A / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9Y265, DNA helicase #10: タンパク質 | 分子量: 51222.465 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RUVBL2, INO80J, TIP48, TIP49B, CGI-46 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9Y230, DNA helicase #11: タンパク質 | 分子量: 41782.660 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ACTB / 発現宿主: Homo sapiens (ヒト) 参照: UniProt: P60709, 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 #12: 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 #13: タンパク質 | | 分子量: 53090.699 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: DMAP1, KIAA1425 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9NPF5 #14: タンパク質 | | 分子量: 26541.537 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: YEATS4, GAS41 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: O95619 |
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-DNA鎖 , 2種, 2分子 XY
#15: DNA鎖 | 分子量: 45644.070 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) |
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#16: DNA鎖 | 分子量: 45105.727 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) |
-非ポリマー , 4種, 11分子
#17: 化合物 | ChemComp-ADP / #18: 化合物 | ChemComp-MG / | #19: 化合物 | ChemComp-BEF / | #20: 化合物 | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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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: Structure of nucleosome-bound SRCAP-C in the ADP-BeFx-bound state タイプ: COMPLEX / Entity ID: #4-#6, #8-#12, #14, #1-#3, #7, #13, #15-#16 / 由来: MULTIPLE SOURCES |
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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: 8 |
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: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 1500 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 (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: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 475617 / 対称性のタイプ: POINT |