+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7tb3 | ||||||||||||
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タイトル | cryo-EM structure of MBP-KIX-apoferritin | ||||||||||||
要素 | Isoform 2 of CREB-binding protein,Ferritin heavy chain, N-terminally processed | ||||||||||||
キーワード | STRUCTURAL PROTEIN / Protein Engineering / Simulation / Peptide Therapeutics / Acute Myeloid Leukemia | ||||||||||||
機能・相同性 | 機能・相同性情報 Iron uptake and transport / Golgi Associated Vesicle Biogenesis / peptide lactyltransferase (CoA-dependent) activity / regulation of smoothened signaling pathway / 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 / iron ion sequestering activity / histone H3K18 acetyltransferase activity ...Iron uptake and transport / Golgi Associated Vesicle Biogenesis / peptide lactyltransferase (CoA-dependent) activity / regulation of smoothened signaling pathway / 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 / iron ion sequestering activity / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / MRF binding / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / FOXO-mediated transcription of cell death genes / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / negative regulation of ferroptosis / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / NFE2L2 regulating anti-oxidant/detoxification enzymes / peptide-lysine-N-acetyltransferase activity / NFE2L2 regulating tumorigenic genes / embryonic digit morphogenesis / homeostatic process / protein acetylation / Notch-HLH transcription pathway / ferroxidase / positive regulation of transforming growth factor beta receptor signaling pathway / autolysosome / Formation of paraxial mesoderm / stimulatory C-type lectin receptor signaling pathway / acetyltransferase activity / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / ferroxidase activity / intracellular sequestering of iron ion / histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / Attenuation phase / cellular response to nutrient levels / Transcriptional and post-translational regulation of MITF-M expression and activity / canonical NF-kappaB signal transduction / histone acetyltransferase activity / regulation of cellular response to heat / negative regulation of fibroblast proliferation / 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 / Regulation of lipid metabolism by PPARalpha / NPAS4 regulates expression of target genes / CD209 (DC-SIGN) signaling / autophagosome / Neutrophil degranulation / ferric iron binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / protein destabilization / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / ferrous iron binding / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / transcription coactivator binding / Pre-NOTCH Transcription and Translation / Transcriptional regulation of white adipocyte differentiation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of protein localization to nucleus / Activation of anterior HOX genes in hindbrain development during early embryogenesis / transcription corepressor activity / cellular response to UV / rhythmic process / p53 binding / Circadian Clock / TRAF3-dependent IRF activation pathway / HATs acetylate histones / iron ion transport / protein-containing complex assembly / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / damaged DNA binding / transcription coactivator activity 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: 2.57 Å | ||||||||||||
データ登録者 | 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 | 米国, 3件
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引用 | ジャーナル: ACS Cent Sci / 年: 2022 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 |
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 | 7tb3.cif.gz | 1002 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7tb3.ent.gz | 852.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7tb3.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 | 7tb3_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7tb3_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | 7tb3_validation.xml.gz | 136.9 KB | 表示 | |
CIF形式データ | 7tb3_validation.cif.gz | 184.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/tb/7tb3 ftp://data.pdbj.org/pub/pdb/validation_reports/tb/7tb3 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 30408.438 Da / 分子数: 24 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CREBBP, CBP, Fth1, Fth 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: Q92793, UniProt: P09528, histone acetyltransferase, 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 Has protein modification | 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: MBP-KIX-apoferritin / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT |
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分子量 | 値: 1.7 MDa / 実験値: YES |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) |
緩衝液 | pH: 8 |
試料 | 濃度: 4 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: MBP-KIX-apoferritin |
試料支持 | グリッドのタイプ: Quantifoil R2/1 |
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 / 倍率(公称値): 165000 X / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 300 nm / Cs: 2.7 mm / C2レンズ絞り径: 70 µm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 6 sec. / 電子線照射量: 43.8 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 撮影したグリッド数: 1 / 実像数: 1915 |
電子光学装置 | 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 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 167662 | ||||||||||||||||||||||||
対称性 | 点対称性: O (正8面体型対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 2.57 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 37386 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | プロトコル: OTHER / Target criteria: Q-score |