+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6kiu | ||||||
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タイトル | Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) | ||||||
要素 |
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キーワード | TRANSCRIPTION/DNA / histone modification (ヒストン) / nucleosome (ヌクレオソーム) / MLL / TRANSCRIPTION (転写 (生物学)) / TRANSCRIPTION-DNA complex | ||||||
機能・相同性 | 機能・相同性情報 protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of short-term neuronal synaptic plasticity / MLL3/4 complex / Set1C/COMPASS complex / exploration behavior ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / regulation of short-term neuronal synaptic plasticity / MLL3/4 complex / Set1C/COMPASS complex / exploration behavior / MLL1/2 complex / ATAC complex / definitive hemopoiesis / NSL complex / histone H3K4 methyltransferase activity / T-helper 2 cell differentiation / : / Cardiogenesis / Formation of the ternary complex, and subsequently, the 43S complex / embryonic hemopoiesis / anterior/posterior pattern specification / Ribosomal scanning and start codon recognition / histone methyltransferase complex / regulation of tubulin deacetylation / Translation initiation complex formation / : / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / SARS-CoV-1 modulates host translation machinery / minor groove of adenine-thymine-rich DNA binding / Peptide chain elongation / Selenocysteine synthesis / 脱分極 / MLL1 complex / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / regulation of embryonic development / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / 造血 / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / histone acetyltransferase complex / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / epigenetic regulation of gene expression / positive regulation of gluconeogenesis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / spleen development / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / transcription initiation-coupled chromatin remodeling / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / グリコーゲン合成 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / cellular response to transforming growth factor beta stimulus / methylated histone binding / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / APC-Cdc20 mediated degradation of Nek2A / cytosolic ribosome / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLI 類似検索 - 分子機能 | ||||||
生物種 | Xenopus laevis (アフリカツメガエル) Homo sapiens (ヒト) synthetic construct (人工物) | ||||||
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 | Huang, J. / Xue, H. / Yao, T. | ||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Nature / 年: 2019 タイトル: Structural basis of nucleosome recognition and modification by MLL methyltransferases. 著者: Han Xue / Tonghui Yao / Mi Cao / Guanjun Zhu / Yan Li / Guiyong Yuan / Yong Chen / Ming Lei / Jing Huang / 要旨: Methyltransferases of the mixed-lineage leukaemia (MLL) family-which include MLL1, MLL2, MLL3, MLL4, SET1A and SET1B-implement methylation of histone H3 on lysine 4 (H3K4), and have critical and ...Methyltransferases of the mixed-lineage leukaemia (MLL) family-which include MLL1, MLL2, MLL3, MLL4, SET1A and SET1B-implement methylation of histone H3 on lysine 4 (H3K4), and have critical and distinct roles in the regulation of transcription in haematopoiesis, adipogenesis and development. The C-terminal catalytic SET (Su(var.)3-9, enhancer of zeste and trithorax) domains of MLL proteins are associated with a common set of regulatory factors (WDR5, RBBP5, ASH2L and DPY30) to achieve specific activities. Current knowledge of the regulation of MLL activity is limited to the catalysis of histone H3 peptides, and how H3K4 methyl marks are deposited on nucleosomes is poorly understood. H3K4 methylation is stimulated by mono-ubiquitination of histone H2B on lysine 120 (H2BK120ub1), a prevalent histone H2B mark that disrupts chromatin compaction and favours open chromatin structures, but the underlying mechanism remains unknown. Here we report cryo-electron microscopy structures of human MLL1 and MLL3 catalytic modules associated with nucleosome core particles that contain H2BK120ub1 or unmodified H2BK120. These structures demonstrate that the MLL1 and MLL3 complexes both make extensive contacts with the histone-fold and DNA regions of the nucleosome; this allows ease of access to the histone H3 tail, which is essential for the efficient methylation of H3K4. The H2B-conjugated ubiquitin binds directly to RBBP5, orienting the association between MLL1 or MLL3 and the nucleosome. The MLL1 and MLL3 complexes display different structural organizations at the interface between the WDR5, RBBP5 and MLL1 (or the corresponding MLL3) subunits, which accounts for the opposite roles of WDR5 in regulating the activity of the two enzymes. These findings transform our understanding of the structural basis for the regulation of MLL activity at the nucleosome level, and highlight the pivotal role of nucleosome regulation in histone-tail modification. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6kiu.cif.gz | 569.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6kiu.ent.gz | 419.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6kiu.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ki/6kiu ftp://data.pdbj.org/pub/pdb/validation_reports/ki/6kiu | HTTPS FTP |
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-関連構造データ
関連構造データ | 9998MC 0693C 0694C 0695C 9999C 6kivC 6kiwC 6kixC 6kizC 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 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-タンパク質 , 9種, 13分子 AEBFCGDHKNRTO
#1: タンパク質 | 分子量: 15303.930 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Xenopus laevis (アフリカツメガエル) 遺伝子: XELAEV_18002543mg / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A310TTQ1, UniProt: P84233*PLUS #2: タンパク質 | 分子量: 11263.231 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Xenopus laevis (アフリカツメガエル) 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62799 #3: タンパク質 | 分子量: 13978.241 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Xenopus laevis (アフリカツメガエル) 遺伝子: hist1h2aj, LOC494591, XELAEV_18003602mg / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q6AZJ8, UniProt: P06897*PLUS #4: タンパク質 | 分子量: 13498.715 Da / 分子数: 2 / Mutation: S29T/K117T / 由来タイプ: 組換発現 由来: (組換発現) Xenopus laevis (アフリカツメガエル) 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P02281 #7: タンパク質 | | 分子量: 24970.539 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: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1 / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: Q03164, ヒストンメチルトランスフェラーゼ #8: タンパク質 | | 分子量: 59223.477 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: RBBP5, RBQ3 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q15291 #9: タンパク質 | | 分子量: 36635.438 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: WDR5, BIG3 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P61964 #10: タンパク質 | | 分子量: 60288.758 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: ASH2L, ASH2L1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9UBL3 #11: タンパク質 | | 分子量: 8622.922 Da / 分子数: 1 / Mutation: G76C / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RPS27A, UBA80, UBCEP1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62979 |
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-DNA鎖 , 2種, 2分子 IJ
#5: DNA鎖 | 分子量: 44521.367 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
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#6: DNA鎖 | 分子量: 44992.648 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
-非ポリマー , 4種, 4分子
#12: 化合物 | ChemComp-SAH / |
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#13: 化合物 | ChemComp-ZN / |
#14: 化合物 | ChemComp-LYS / |
#15: 化合物 | ChemComp-GLN / |
-詳細
研究の焦点であるリガンドがあるか | N |
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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 |
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由来(天然) |
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由来(組換発現) |
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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: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy |
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
ソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||
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: 139535 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
精密化 | 立体化学のターゲット値: GeoStd + Monomer Library | ||||||||||||||||||||||||
拘束条件 |
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