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基本情報
登録情報 | データベース: EMDB / ID: EMD-25799 | ||||||||||||
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タイトル | cryo-EM structure of MBP-KIX-apoferritin complex with peptide 7 | ||||||||||||
![]() | cryo-EM structure of MBP-KIX-apoferritin complex with peptide 7 | ||||||||||||
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機能・相同性 | ![]() Iron uptake and transport / Golgi Associated Vesicle Biogenesis / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / iron ion sequestering activity / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / negative regulation of ferroptosis / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / autolysosome / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / embryonic digit morphogenesis / homeostatic process / protein acetylation / ferroxidase / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / intracellular sequestering of iron ion / histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / Transcriptional and post-translational regulation of MITF-M expression and activity / ferroxidase activity / Attenuation phase / cellular response to nutrient levels / canonical NF-kappaB signal transduction / regulation of cellular response to heat / negative regulation of fibroblast proliferation / histone acetyltransferase activity / histone acetyltransferase / endocytic vesicle lumen / 転移酵素; アシル基を移すもの; アミノアシル基以外のアシル基を移すもの / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / CD209 (DC-SIGN) signaling / Neutrophil degranulation / ferric iron binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Formation of the beta-catenin:TCF transactivating complex / PPARA activates gene expression / Heme signaling / protein destabilization / ferrous iron binding / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / Evasion by RSV of host interferon responses / chromatin DNA binding / p53 binding / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / transcription coactivator binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of protein localization to nucleus / rhythmic process / transcription corepressor activity / cellular response to UV / Circadian Clock / HATs acetylate histones / TRAF3-dependent IRF activation pathway / iron ion transport / DNA-binding transcription factor binding / transcription regulator complex / protein-containing complex assembly / Estrogen-dependent gene expression / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / response to hypoxia 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.3 Å | ||||||||||||
![]() | Zhang K / Horikoshi N / Li S / Powers A / Hameedi M / Pintilie G / Chae H / Khan Y / Suomivuori C / Dror R ...Zhang K / Horikoshi N / Li S / Powers A / Hameedi M / Pintilie G / Chae H / Khan Y / Suomivuori C / Dror R / Sakamoto K / Chiu W / Wakatsuki S | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Cryo-EM, Protein Engineering, and Simulation Enable the Development of Peptide Therapeutics against Acute Myeloid Leukemia. 著者: Kaiming Zhang / Naoki Horikoshi / Shanshan Li / Alexander S Powers / Mikhail A Hameedi / Grigore D Pintilie / Hee-Don Chae / Yousuf A Khan / Carl-Mikael Suomivuori / Ron O Dror / Kathleen M ...著者: Kaiming Zhang / Naoki Horikoshi / Shanshan Li / Alexander S Powers / Mikhail A Hameedi / Grigore D Pintilie / Hee-Don Chae / Yousuf A Khan / Carl-Mikael Suomivuori / Ron O Dror / Kathleen M Sakamoto / Wah Chiu / Soichi Wakatsuki / ![]() ![]() ![]() 要旨: Cryogenic electron microscopy (cryo-EM) has emerged as a viable structural tool for molecular therapeutics development against human diseases. However, it remains a challenge to determine structures ...Cryogenic electron microscopy (cryo-EM) has emerged as a viable structural tool for molecular therapeutics development against human diseases. However, it remains a challenge to determine structures of proteins that are flexible and smaller than 30 kDa. The 11 kDa KIX domain of CREB-binding protein (CBP), a potential therapeutic target for acute myeloid leukemia and other cancers, is a protein which has defied structure-based inhibitor design. Here, we develop an experimental approach to overcome the size limitation by engineering a protein double-shell to sandwich the KIX domain between apoferritin as the inner shell and maltose-binding protein as the outer shell. To assist homogeneous orientations of the target, disulfide bonds are introduced at the target-apoferritin interface, resulting in a cryo-EM structure at 2.6 Å resolution. We used molecular dynamics simulations to design peptides that block the interaction of the KIX domain of CBP with the intrinsically disordered pKID domain of CREB. The double-shell design allows for fluorescence polarization assays confirming the binding between the KIX domain in the double-shell and these interacting peptides. Further cryo-EM analysis reveals a helix-helix interaction between a single KIX helix and the best peptide, providing a possible strategy for developments of next-generation inhibitors. | ||||||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 107 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 14.4 KB 14.4 KB | 表示 表示 | ![]() |
画像 | ![]() | 85.4 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | cryo-EM structure of MBP-KIX-apoferritin complex with peptide 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.82 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
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試料の構成要素
-全体 : MBP-KIX-apoferritin complex with peptide 7
全体 | 名称: MBP-KIX-apoferritin complex with peptide 7 |
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要素 |
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-超分子 #1: MBP-KIX-apoferritin complex with peptide 7
超分子 | 名称: MBP-KIX-apoferritin complex with peptide 7 / タイプ: complex / キメラ: Yes / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: ![]() |
組換発現 | 生物種: ![]() ![]() |
分子量 | 実験値: 1.7 MDa |
-分子 #1: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-termina...
分子 | 名称: Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed タイプ: protein_or_peptide / ID: 1 / コピー数: 24 / 光学異性体: LEVO / EC番号: histone acetyltransferase |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 30.408438 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: HMGVRKGWHE HVTQDLRSHL VHKLVQAIFP CPDPCALKDR RMENLVAYAK KVEGDMYESA NSRDEYYHLL AEKIYKIQKE LEEKSQVRQ NYHQDAEAAI NRQINLELYA SYVYLSMSCY FDRDDVALKN FAKYFLHQSH EEREHAEKLM KLQNQRGGRI F LQDIKKPD ...文字列: HMGVRKGWHE HVTQDLRSHL VHKLVQAIFP CPDPCALKDR RMENLVAYAK KVEGDMYESA NSRDEYYHLL AEKIYKIQKE LEEKSQVRQ NYHQDAEAAI NRQINLELYA SYVYLSMSCY FDRDDVALKN FAKYFLHQSH EEREHAEKLM KLQNQRGGRI F LQDIKKPD RDDWCSGLNA MESALHLEKS VNQSLLELHK LATDKNDPHL CDFIETYYLS EQVKSIKELG DHVTNLRKMG AP CAGMAEY LFDKHTLGHG DES |
-分子 #2: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-A...
分子 | 名称: LEU-SER-ARG-ARG-PRO-SEP-TYR-ARG-LYS-ILE-LEU-ASN-ASP-LEU-SER-SER-ASP-ALA-PRO タイプ: protein_or_peptide / ID: 2 / コピー数: 24 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 2.272457 KDa |
配列 | 文字列: LSRRP(SEP)YRKI LNDLSSDAP |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 4 mg/mL |
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緩衝液 | pH: 8 |
グリッド | モデル: Quantifoil R2/1 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY |
凍結 | 凍結剤: ETHANE |
詳細 | MBP-KIX-apoferritin complex with peptide 7 |
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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 |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 撮影したグリッド数: 1 / 実像数: 2490 / 平均露光時間: 6.0 sec. / 平均電子線量: 43.8 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 70.0 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): 0.3 µm / 倍率(公称値): 165000 |
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 |
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画像解析
-原子モデル構築 1
精密化 | プロトコル: OTHER / 当てはまり具合の基準: Q-score |
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得られたモデル | ![]() PDB-7tbh: |