National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R35GM128777
米国
National Institutes of Health/National Institute on Aging (NIH/NIA)
R01AG063845
米国
引用
ジャーナル: bioRxiv / 年: 2023 タイトル: Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. 著者: Natasha I Edman / Rachel L Redler / Ashish Phal / Thomas Schlichthaerle / Sanjay R Srivatsan / Ali Etemadi / Seong J An / Andrew Favor / Devon Ehnes / Zhe Li / Florian Praetorius / Max Gordon ...著者: Natasha I Edman / Rachel L Redler / Ashish Phal / Thomas Schlichthaerle / Sanjay R Srivatsan / Ali Etemadi / Seong J An / Andrew Favor / Devon Ehnes / Zhe Li / Florian Praetorius / Max Gordon / Wei Yang / Brian Coventry / Derrick R Hicks / Longxing Cao / Neville Bethel / Piper Heine / Analisa Murray / Stacey Gerben / Lauren Carter / Marcos Miranda / Babak Negahdari / Sangwon Lee / Cole Trapnell / Lance Stewart / Damian C Ekiert / Joseph Schlessinger / Jay Shendure / Gira Bhabha / Hannele Ruohola-Baker / David Baker / 要旨: Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, ...Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affects signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a designed fibroblast growth-factor receptor (FGFR) binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation. The high specificity of the designed agonists reveal distinct roles for two FGFR splice variants in driving endothelial and mesenchymal cell fates during early vascular development. The ability to incorporate receptor binding domains and repeat extensions in a modular fashion makes our designed scaffolds broadly useful for probing and manipulating cellular signaling pathways.
名称: Self-assembled homo-octamer of de novo designed protein C8-71 タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT
由来(天然)
生物種: synthetic construct (人工物)
由来(組換発現)
生物種: Escherichia coli BL21 (大腸菌)
緩衝液
ID
Specimen-ID
pH
1
1
8
2
2
8
試料
Experiment-ID: 1 / 濃度: 0.9 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: Sample present within the ice layer as both isolated homo-octameric rings and fibrils of variable length
ID
1
2
試料支持
ID
Specimen-ID
グリッドの材料
グリッドのサイズ (divisions/in.)
グリッドのタイプ
詳細
1
1
COPPER
300
Quantifoil R2/2
2
2
COPPER
300
Quantifoil R1.2/1.3
No pre-treatment
急速凍結
凍結前の試料温度: 295 K / 凍結剤: ETHANE / 詳細: blot time = 4s; blot force = 0 / Entry-ID: 8F6Q / 湿度: 100 % / 装置: FEI VITROBOT MARK IV
モード: BRIGHT FIELD / 倍率(公称値): 81000 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): 800 nm
試料ホルダ
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影
平均露光時間: 2.5 sec. / 電子線照射量: 61.3 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 2 / 実像数: 3092
-
解析
ソフトウェア
名称
バージョン
分類
NB
phenix.real_space_refine
1.16_3549
精密化
PHENIX
1.16_3549
精密化
EMソフトウェア
ID
名称
バージョン
カテゴリ
詳細
1
cryoSPARC
粒子像選択
2
Leginon
画像取得
4
cryoSPARC
CTF補正
CTFFIND
7
UCSF Chimera
モデルフィッティング
9
cryoSPARC
初期オイラー角割当
10
cryoSPARC
最終オイラー角割当
12
cryoSPARC
3次元再構成
13
PHENIX
1.16
モデル精密化
CTF補正
タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性
点対称性: C8 (8回回転対称)
3次元再構成
解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 132391 / 対称性のタイプ: POINT
原子モデル構築
プロトコル: AB INITIO MODEL / 空間: REAL / Target criteria: Correlation coefficients 詳細: Designed oligomer was used as initial model and was initially fit into map using UCSF Chimera