PDB-7sz7: Cryo-EM structure of the extracellular module of the full-length ...

基本情報

• 登録情報: データベース: PDB / ID: 7sz7
• タイトル: Cryo-EM structure of the extracellular module of the full-length EGFR bound to TGF-alpha. "tips-juxtaposed" conformation

要素

• Epidermal growth factor receptor
• Transforming growth factor alpha

• キーワード: SIGNALING PROTEIN / Transferase / receptor tyrosine kinases / epidermal growth factor receptor

機能・相同性

分子機能:

hepatocyte proliferation / Cargo concentration in the ER / response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of protein kinase C activity / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / COPII-mediated vesicle transport / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / tongue development / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / epidermal growth factor binding / response to UV-A / PLCG1 events in ERBB2 signaling / midgut development / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / hydrogen peroxide metabolic process / ERBB2-EGFR signaling pathway / epidermal growth factor receptor binding / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / response to cobalamin / Signaling by ERBB4 / eyelid development in camera-type eye / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / positive regulation of cell division / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / hair follicle development / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / mammary gland alveolus development / embryonic placenta development / positive regulation of bone resorption / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / positive regulation of phosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / endoplasmic reticulum-Golgi intermediate compartment membrane / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / cellular response to epidermal growth factor stimulus / EGFR Transactivation by Gastrin / transmembrane receptor protein tyrosine kinase activity / cellular response to cadmium ion / GRB2 events in ERBB2 signaling / positive regulation of DNA repair / neurogenesis / SHC1 events in ERBB2 signaling / regulation of ERK1 and ERK2 cascade / positive regulation of mitotic nuclear division / cellular response to dexamethasone stimulus / ossification / positive regulation of synaptic transmission, glutamatergic / positive regulation of epithelial cell proliferation / neuron projection morphogenesis / epithelial cell proliferation / basal plasma membrane / positive regulation of superoxide anion generation / positive regulation of DNA replication / Signal transduction by L1 / cellular response to estradiol stimulus / liver regeneration / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / positive regulation of protein localization to plasma membrane / cellular response to amino acid stimulus / lung development / Signaling by ERBB2 TMD/JMD mutants / positive regulation of smooth muscle cell proliferation / EGFR downregulation / growth factor activity / positive regulation of MAP kinase activity / clathrin-coated endocytic vesicle membrane / Constitutive Signaling by EGFRvIII / negative regulation of protein catabolic process / Signaling by ERBB2 ECD mutants

ドメイン・相同性:

: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / EGF-like domain profile. / : / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily

構成要素:

Epidermal growth factor receptor / Protransforming growth factor alpha

• 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: 3.4 Å
• データ登録者: Huang, Y. / Ognjenovic, J. / Karandur, D. / Miller, K. / Merk, A. / Subramaniam, S. / Kuriyan, J.

資金援助

カナダ, 米国, 2件

組織	認可番号	国
Canada Excellence Research Chair Award		カナダ
Howard Hughes Medical Institute (HHMI)		米国

• 引用: ジャーナル: Elife / 年: 2021; タイトル: A molecular mechanism for the generation of ligand-dependent differential outputs by the epidermal growth factor receptor.; 著者: Yongjian Huang / Jana Ognjenovic / Deepti Karandur / Kate Miller / Alan Merk / Sriram Subramaniam / John Kuriyan / ; 要旨: The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that couples the binding of extracellular ligands, such as EGF and transforming growth factor-α (TGF-α), to the initiation of intracellular signaling pathways. EGFR binds to EGF and TGF-α with similar affinity, but generates different signals from these ligands. To address the mechanistic basis of this phenomenon, we have carried out cryo-EM analyses of human EGFR bound to EGF and TGF-α. We show that the extracellular module adopts an ensemble of dimeric conformations when bound to either EGF or TGF-α. The two extreme states of this ensemble represent distinct ligand-bound quaternary structures in which the membrane-proximal tips of the extracellular module are either juxtaposed or separated. EGF and TGF-α differ in their ability to maintain the conformation with the membrane-proximal tips of the extracellular module separated, and this conformation is stabilized preferentially by an oncogenic EGFR mutation. Close proximity of the transmembrane helices at the junction with the extracellular module has been associated previously with increased EGFR activity. Our results show how EGFR can couple the binding of different ligands to differential modulation of this proximity, thereby suggesting a molecular mechanism for the generation of ligand-sensitive differential outputs in this receptor family.

履歴

登録	2021年11月25日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2021年12月15日	Provider: repository / タイプ: Initial release

集合体

登録構造単位

A: Epidermal growth factor receptor

C: Transforming growth factor alpha

B: Epidermal growth factor receptor

D: Transforming growth factor alpha

概要:

• 280 kDa, 4 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	279,987	4
ポリマ－	279,987	4
非ポリマー	0	0
水	0	0

1

概要:

• 登録構造と同一
• 登録者が定義した集合体
• 根拠: 電子顕微鏡法

対称操作:

タイプ	名称	対称操作	数
identity operation	1_555		1

要素

#1: タンパク質

A B Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1

詳細:

分子量: 134433.328 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EGFR, ERBB, ERBB1, HER1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P00533, receptor protein-tyrosine kinase

#2: タンパク質・ペプチド

C D Transforming growth factor alpha / TGF-alpha / EGF-like TGF / ETGF / TGF type 1

詳細:

分子量: 5560.246 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TGFA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01135

実験情報

実験

• 実験: 手法: 電子顕微鏡法
• 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: full-length human EGFR:TGF-alpha complex / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT
• 分子量: 実験値: NO
• 由来(天然): 生物種: Homo sapiens (ヒト)
• 由来(組換発現): 生物種: Homo sapiens (ヒト)
• 緩衝液: pH: 8
• 試料: 濃度: 0.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
• 試料支持: グリッドのタイプ: UltrAuFoil R1.2/1.3
• 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
• 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
• 撮影: 電子線照射量: 50 e/Ų / フィルム・検出器のモデル: GATAN K3 (6k x 4k)

解析

EMソフトウェア

ID	名称	バージョン	カテゴリ
10	cryoSPARC	v2	初期オイラー角割当
11	cryoSPARC	v2	最終オイラー角割当
12	cryoSPARC	v2	分類
13	cryoSPARC	v2	３次元再構成

• CTF補正: タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
• 対称性: 点対称性: C₁ (非対称)
• 3次元再構成: 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 126471 / 対称性のタイプ: POINT