+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-22265 | |||||||||||||||
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タイトル | Cryo-EM structure of BCL6 bound to BI-3802 | |||||||||||||||
マップデータ | Main map | |||||||||||||||
試料 |
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キーワード | transcription factor / degrader / TRANSCRIPTION | |||||||||||||||
機能・相同性 | 機能・相同性情報 regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation ...regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation / plasma cell differentiation / paraspeckles / germinal center formation / pyramidal neuron differentiation / regulation of immune system process / type 2 immune response / positive regulation of regulatory T cell differentiation / T-helper 2 cell differentiation / negative regulation of B cell apoptotic process / positive regulation of cell motility / negative regulation of Rho protein signal transduction / FOXO-mediated transcription of cell death genes / negative regulation of cell-matrix adhesion / regulation of T cell proliferation / negative regulation of Notch signaling pathway / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / B cell proliferation / regulation of cell differentiation / negative regulation of cellular senescence / Rho protein signal transduction / regulation of immune response / erythrocyte development / heterochromatin formation / positive regulation of B cell proliferation / regulation of cytokine production / positive regulation of neuron differentiation / cell-matrix adhesion / transcription corepressor binding / cell motility / cell morphogenesis / protein localization / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / regulation of inflammatory response / actin cytoskeleton organization / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / inflammatory response / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding 類似検索 - 分子機能 | |||||||||||||||
生物種 | Homo sapiens (ヒト) | |||||||||||||||
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 | Yoon H / Burman SSR | |||||||||||||||
資金援助 | 米国, スイス, 4件
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引用 | ジャーナル: Nature / 年: 2020 タイトル: Small-molecule-induced polymerization triggers degradation of BCL6. 著者: Mikołaj Słabicki / Hojong Yoon / Jonas Koeppel / Lena Nitsch / Shourya S Roy Burman / Cristina Di Genua / Katherine A Donovan / Adam S Sperling / Moritz Hunkeler / Jonathan M Tsai / Rohan ...著者: Mikołaj Słabicki / Hojong Yoon / Jonas Koeppel / Lena Nitsch / Shourya S Roy Burman / Cristina Di Genua / Katherine A Donovan / Adam S Sperling / Moritz Hunkeler / Jonathan M Tsai / Rohan Sharma / Andrew Guirguis / Charles Zou / Priya Chudasama / Jessica A Gasser / Peter G Miller / Claudia Scholl / Stefan Fröhling / Radosław P Nowak / Eric S Fischer / Benjamin L Ebert / 要旨: Effective and sustained inhibition of non-enzymatic oncogenic driver proteins is a major pharmacological challenge. The clinical success of thalidomide analogues demonstrates the therapeutic efficacy ...Effective and sustained inhibition of non-enzymatic oncogenic driver proteins is a major pharmacological challenge. The clinical success of thalidomide analogues demonstrates the therapeutic efficacy of drug-induced degradation of transcription factors and other cancer targets, but a substantial subset of proteins are resistant to targeted degradation using existing approaches. Here we report an alternative mechanism of targeted protein degradation, in which a small molecule induces the highly specific, reversible polymerization of a target protein, followed by its sequestration into cellular foci and subsequent degradation. BI-3802 is a small molecule that binds to the Broad-complex, Tramtrack and Bric-à-brac (BTB) domain of the oncogenic transcription factor B cell lymphoma 6 (BCL6) and leads to the proteasomal degradation of BCL6. We use cryo-electron microscopy to reveal how the solvent-exposed moiety of a BCL6-binding molecule contributes to a composite ligand-protein surface that engages BCL6 homodimers to form a supramolecular structure. Drug-induced formation of BCL6 filaments facilitates ubiquitination by the SIAH1 E3 ubiquitin ligase. Our findings demonstrate that a small molecule such as BI-3802 can induce polymerization coupled to highly specific protein degradation, which in the case of BCL6 leads to increased pharmacological activity compared to the effects induced by other BCL6 inhibitors. These findings open new avenues for the development of therapeutic agents and synthetic biology. | |||||||||||||||
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_22265.map.gz | 4.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-22265-v30.xml emd-22265.xml | 21.9 KB 21.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_22265_fsc.xml | 9.2 KB | 表示 | FSCデータファイル |
画像 | emd_22265.png | 39 KB | ||
マスクデータ | emd_22265_msk_1.map | 64 MB | マスクマップ | |
Filedesc metadata | emd-22265.cif.gz | 7 KB | ||
その他 | emd_22265_half_map_1.map.gz emd_22265_half_map_2.map.gz | 49.6 MB 49.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-22265 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22265 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_22265_validation.pdf.gz | 802.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_22265_full_validation.pdf.gz | 802.4 KB | 表示 | |
XML形式データ | emd_22265_validation.xml.gz | 16 KB | 表示 | |
CIF形式データ | emd_22265_validation.cif.gz | 21 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22265 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22265 | 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_22265.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.825 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
-マスク #1
ファイル | emd_22265_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: unfiltered half map (1) from refinement
ファイル | emd_22265_half_map_1.map | ||||||||||||
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注釈 | unfiltered half map (1) from refinement | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: unfiltered half map (2) from refinement
ファイル | emd_22265_half_map_2.map | ||||||||||||
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注釈 | unfiltered half map (2) from refinement | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : B-cell lymphoma 6 protein (BCL6) filament
全体 | 名称: B-cell lymphoma 6 protein (BCL6) filament |
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要素 |
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-超分子 #1: B-cell lymphoma 6 protein (BCL6) filament
超分子 | 名称: B-cell lymphoma 6 protein (BCL6) filament / タイプ: organelle_or_cellular_component / ID: 1 / 親要素: 0 / 含まれる分子: #1 詳細: BCL6 polymerized upon addition of small molecule BI-3802. 4 dimers enclosed in map. |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 352 KDa |
-分子 #1: B-cell lymphoma 6 protein
分子 | 名称: B-cell lymphoma 6 protein / タイプ: protein_or_peptide / ID: 1 / コピー数: 8 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 44.505305 KDa |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
配列 | 文字列: MDWSHPQFEK SAVGLNDIFE AQKIEWHEGG GGSGENLYFQ GGGRADSCIQ FTRHASDVLL NLNRLRSRDI LTDVVIVVSR EQFRAHKTV LMACSGLFYS IFTDQLKCNL SVINLDPEIN PEGFCILLDF MYTSRLNLRE GNIMAVMATA MYLQMEHVVD T CRKFIKAS ...文字列: MDWSHPQFEK SAVGLNDIFE AQKIEWHEGG GGSGENLYFQ GGGRADSCIQ FTRHASDVLL NLNRLRSRDI LTDVVIVVSR EQFRAHKTV LMACSGLFYS IFTDQLKCNL SVINLDPEIN PEGFCILLDF MYTSRLNLRE GNIMAVMATA MYLQMEHVVD T CRKFIKAS EAEMVSAIKP PREEFLNSRM LMPQDIMAYR GCEVVENNLP LRSAPGCESR AFAPSLYSGL STPPASYSMY SH LPVSSLL FSDEEFRDVR MPVANPFPKE RALPCDSARP VPGEYSRPTL EVSPNVCHSN IYSPKETIPE EARSDMHYSV AEG LKPAAP SARNAPYFPC DKASKEEERP SSEDEIALHF EPPNAPLNRK GLVSPQSPQK SDCQPNSPTE SCSSKNACIL QASG UniProtKB: B-cell lymphoma 6 protein |
-分子 #2: 2-[6-[[5-chloranyl-2-[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]py...
分子 | 名称: 2-[6-[[5-chloranyl-2-[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]pyrimidin-4-yl]amino]-1-methyl-2-oxidanylidene-quinolin-3-yl]oxy-~{N}-methyl-ethanamide タイプ: ligand / ID: 2 / コピー数: 8 / 式: U52 |
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分子量 | 理論値: 484.978 Da |
Chemical component information | ChemComp-U52: |
-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 | filament |
-試料調製
濃度 | 0.48 mg/mL | ||||||||||||
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緩衝液 | pH: 7.4 構成要素:
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / 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 / 支持フィルム - Film thickness: 12 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 60 sec. / 前処理 - 雰囲気: AIR / 前処理 - 気圧: 0.039 kPa | ||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 283.15 K / 装置: LEICA EM GP / 詳細: 4 ul sample applied twice, blotted 1.3s each time. | ||||||||||||
詳細 | Strep II-Avi BCL6 (aa5-360) polymerized by addition of 1.5 molar excess BI-3802. CHAPSO (0.8 mM final) added for grid preparation. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV |
詳細 | Data collection in counting mode, using multi shot scheme (4 holes per stage position, 2 shots per hole) |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) デジタル化 - サイズ - 横: 5760 pixel / デジタル化 - サイズ - 縦: 4092 pixel / 撮影したグリッド数: 1 / 実像数: 7553 / 平均露光時間: 3.0 sec. / 平均電子線量: 63.4 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): -2.5 µm / 最小 デフォーカス(公称値): -1.0 µm / 倍率(公称値): 105000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
初期モデル | PDB ID: Chain - Chain ID: A / Chain - Residue range: 7-128 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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詳細 | Real_space_refine: global minimization, rigid body and adp refinement with target restraints. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
得られたモデル | PDB-6xmx: |