+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8q6j | |||||||||
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タイトル | Atomic structure and conformational variability of the HER2-Trastuzumab-Pertuzumab complex | |||||||||
要素 |
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キーワード | STRUCTURAL PROTEIN / ErbB-2 / Pertuzumab / Trastuzumab / Ternary complex / Protein / Flexibility / Continuous conformation / Cryo-EM / Single particle analysis | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / semaphorin receptor complex / ErbB-3 class receptor binding / regulation of microtubule-based process / Sema4D induced cell migration and growth-cone collapse ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / semaphorin receptor complex / ErbB-3 class receptor binding / regulation of microtubule-based process / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / PLCG1 events in ERBB2 signaling / positive regulation of Rho protein signal transduction / ERBB2-EGFR signaling pathway / ERBB2 Activates PTK6 Signaling / neuromuscular junction development / positive regulation of transcription by RNA polymerase I / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / enzyme-linked receptor protein signaling pathway / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / positive regulation of protein targeting to membrane / regulation of angiogenesis / coreceptor activity / Schwann cell development / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / cellular response to epidermal growth factor stimulus / transmembrane receptor protein tyrosine kinase activity / myelination / GRB2 events in ERBB2 signaling / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neurogenesis / SHC1 events in ERBB2 signaling / regulation of ERK1 and ERK2 cascade / positive regulation of cell adhesion / Downregulation of ERBB2:ERBB3 signaling / Constitutive Signaling by Overexpressed ERBB2 / positive regulation of epithelial cell proliferation / basal plasma membrane / positive regulation of translation / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / wound healing / Signaling by ERBB2 ECD mutants / receptor protein-tyrosine kinase / neuromuscular junction / Signaling by ERBB2 KD Mutants / neuron differentiation / cellular response to growth factor stimulus / receptor tyrosine kinase binding / peptidyl-tyrosine phosphorylation / Downregulation of ERBB2 signaling / ruffle membrane / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / heart development / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / protein tyrosine kinase activity / basolateral plasma membrane / positive regulation of MAPK cascade / early endosome / receptor complex / cell surface receptor signaling pathway / endosome membrane / intracellular signal transduction / positive regulation of protein phosphorylation / protein heterodimerization activity / protein phosphorylation / apical plasma membrane / signaling receptor binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane 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: 3.3 Å | |||||||||
データ登録者 | Ruedas, R. / Vuillemot, R. / Tubiana, T. / Winter, J.M. / Pieri, L. / Arteni, A.A. / Samson, C. / Jonic, J. / Mathieu, M. / Bressanelli, S. | |||||||||
資金援助 | フランス, 2件
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引用 | ジャーナル: J Struct Biol / 年: 2024 タイトル: Structure and conformational variability of the HER2-trastuzumab-pertuzumab complex. 著者: Rémi Ruedas / Rémi Vuillemot / Thibault Tubiana / Jean-Marie Winter / Laura Pieri / Ana-Andreea Arteni / Camille Samson / Slavica Jonic / Magali Mathieu / Stéphane Bressanelli / 要旨: Single particle analysis from cryogenic transmission electron microscopy (cryo-EM) is particularly attractive for complexes for which structure prediction remains intractable, such as antibody- ...Single particle analysis from cryogenic transmission electron microscopy (cryo-EM) is particularly attractive for complexes for which structure prediction remains intractable, such as antibody-antigen complexes. Here we obtain the detailed structure of a particularly difficult complex between human epidermal growth factor receptor 2 (HER2) and the antigen-binding fragments from two distinct therapeutic antibodies binding to distant parts of the flexible HER2, pertuzumab and trastuzumab (HTP). We highlight the strengths and limitations of current data processing software in dealing with various kinds of heterogeneities, particularly continuous conformational heterogeneity, and in describing the motions that can be extracted from our dataset. Our HTP structure provides a more detailed view than the one previously available for this ternary complex. This allowed us to pinpoint a previously overlooked loop in domain IV that may be involved both in binding of trastuzumab and in HER2 dimerization. This finding may contribute to explain the synergistic anticancer effect of the two antibodies. We further propose that the flexibility of the HTP complex, beyond the difficulties it causes for cryo-EM analysis, actually reflects regulation of HER2 signaling and its inhibition by therapeutic antibodies. Notably we obtain our best data with ultra-thin continuous carbon grids, showing that with current cameras their use to alleviate particle misdistribution is compatible with a protein complex of only 162 kDa. Perhaps most importantly, we provide here a dataset for such a smallish protein complex for further development of software accounting for continuous conformational heterogeneity in cryo-EM images. | |||||||||
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 | 8q6j.cif.gz | 298 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8q6j.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 8q6j.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 | 8q6j_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8q6j_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | 8q6j_validation.xml.gz | 59.3 KB | 表示 | |
CIF形式データ | 8q6j_validation.cif.gz | 88.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/q6/8q6j ftp://data.pdbj.org/pub/pdb/validation_reports/q6/8q6j | HTTPS FTP |
-関連構造データ
関連構造データ | 18188MC 8pwhC 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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1 |
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-要素
-タンパク質 , 1種, 1分子 E
#5: タンパク質 | 分子量: 68794.086 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: ERBB2 / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P04626 |
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-抗体 , 4種, 4分子 ABCD
#1: 抗体 | 分子量: 23466.031 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) |
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#2: 抗体 | 分子量: 23425.180 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) |
#3: 抗体 | 分子量: 23548.152 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) |
#4: 抗体 | 分子量: 23674.486 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株 (発現宿主): CHO 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) |
-糖 , 2種, 5分子
#6: 多糖 | #7: 糖 | |
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-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 | 名称: Ternary complex of her2-trastuzumab-pertuzumab Fabs / タイプ: COMPLEX 詳細: Fab fragment from trastuzumab and pertuzumab linked to the extracellular domain of erbb2 (her2) Entity ID: #1-#4 / 由来: RECOMBINANT | |||||||||||||||
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分子量 | 値: 0.171364 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: Homo sapiens (ヒト) / 株: HEK293 / 細胞: human | |||||||||||||||
緩衝液 | pH: 7.5 | |||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.12 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 288.15 K |
-電子顕微鏡撮影
顕微鏡 | モデル: TFS GLACIOS |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 240000 X / 最大 デフォーカス(公称値): 2600 nm / 最小 デフォーカス(公称値): 800 nm / Cs: 2.1 mm / アライメント法: BASIC |
試料ホルダ | 凍結剤: HELIUM 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 4.71 sec. / 電子線照射量: 60 e/Å2 フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 撮影したグリッド数: 1 / 実像数: 8928 |
画像スキャン | 横: 4096 / 縦: 4096 |
-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: 2954825 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 711008 / アルゴリズム: FOURIER SPACE / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 3D fitting-ID: 1
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拘束条件 |
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