EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Disulfi de constrained Fabs overcome target size limitation for high-resolution single-particle cryo-EM.
ジャーナル・号・ページ	bioRxiv, Year 2024
掲載日	2024年5月13日
著者	Jennifer E Kung / Matthew C Johnson / Christine C Jao / Christopher P Arthur / Dimitry Tegunov / Alexis Rohou / Jawahar Sudhamsu /
PubMed 要旨	High-resolution structures of proteins are critical to understanding molecular mechanisms of biological processes and in the discovery of therapeutic molecules. Cryo-EM has revolutionized structure ...High-resolution structures of proteins are critical to understanding molecular mechanisms of biological processes and in the discovery of therapeutic molecules. Cryo-EM has revolutionized structure determination of large proteins and their complexes, but a vast majority of proteins that underlie human diseases are small (< 50 kDa) and usually beyond its reach due to low signal-to-noise images and difficulties in particle alignment. Current strategies to overcome this problem increase the overall size of small protein targets using scaffold proteins that bind to the target, but are limited by inherent flexibility and not being bound to their targets in a rigid manner, resulting in the target being poorly resolved compared to the scaffolds. Here we present an iteratively engineered molecular design for transforming Fabs (antibody fragments), into conformationally rigid scaffolds (Rigid-Fabs) that, when bound to small proteins (~20 kDa), can enable high-resolution structure determination using cryo-EM. This design introduces multiple disulfide bonds at strategic locations, generates a well-folded Fab constrained into a rigid conformation and can be applied to Fabs from various species, isotypes and chimeric Fabs. We present examples of the Rigid Fab design enabling high-resolution (2.3-2.5 Å) structures of small proteins, Ang2 (26 kDa) and KRAS (21 kDa) by cryo-EM. The strategies for designing disulfide constrained Rigid Fabs in our work thus establish a general approach to overcome the target size limitation of single particle cryo-EM.
リンク	bioRxiv / PubMed:38798381 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	2 - 2.9 Å
構造データ	43200 8vgh EMDB-43200, PDB-8vgh: CryoEM structure of tryptase in complex with wild type anti-tryptase Fab E104.v1 手法: EM (単粒子) / 解像度: 2.9 Å 43201 8vgi EMDB-43201, PDB-8vgi: CryoEM structure of tryptase in complex with engineered conformationally rigid anti-tryptase Fab E104.v1.2DS 手法: EM (単粒子) / 解像度: 2.7 Å 43202 8vgj EMDB-43202, PDB-8vgj: CryoEM structure of tryptase in complex with engineered conformationally rigid anti-tryptase Fab E104.v1.4DS 手法: EM (単粒子) / 解像度: 2.5 Å 43203 8vgk EMDB-43203, PDB-8vgk: CryoEM structure of tryptase in complex with engineered conformationally rigid anti-tryptase Fab E104.v1.6DS 手法: EM (単粒子) / 解像度: 2.4 Å 43204 8vgl EMDB-43204: Composite cryoEM map of Nav1.7 in complex with wild type Fab 7A9 PDB-8vgl: CryoEM structure of Nav1.7 in complex with wild type Fab 7A9 手法: EM (単粒子) / 解像度: 2.6 Å EMDB-43205: Consensus cryoEM map of Nav1.7 in complex with wild type Fab 7A9 手法: EM (単粒子) / 解像度: 2.5 Å EMDB-43206: Constituent EM map: Focused refinement of Fab 7A9 in complex of Nav1.7 and Fab 7A9 手法: EM (単粒子) / 解像度: 2.6 Å EMDB-43207: Constituent map: Focused refinement of Nav1.7 in complex of Nav1.7 and Fab 7A9 手法: EM (単粒子) / 解像度: 2.6 Å 43208 8vgm EMDB-43208: Composite cryoEM map of Nav1.7 in complex with engineered conformationally rigid Fab 7A9.4DS PDB-8vgm: CryoEM structure of Nav1.7 in complex with engineered conformationally rigid Fab 7A9.4DS 手法: EM (単粒子) / 解像度: 2.6 Å EMDB-43209: Consensus cryoEM map of Nav1.7 in complex with engineered conformationally rigid Fab 7A9.4DS 手法: EM (単粒子) / 解像度: 2.6 Å EMDB-43210: Constituent map: Focused refinement of Fab 7A9.4DS in complex of Nav1.7 and Fab 7A9.4DS 手法: EM (単粒子) / 解像度: 2.5 Å EMDB-43211: Constituent map: Focused refinement of Nav1.7 in complex of Nav1.7 and Fab 7A9.4DS 手法: EM (単粒子) / 解像度: 2.5 Å 43212 8vgn EMDB-43212: Composite cryoEM map of CD20 in complex with wild type Rituximab Fab PDB-8vgn: CryoEM structure of CD20 in complex with wild type Rituximab Fab 手法: EM (単粒子) / 解像度: 2.5 Å EMDB-43213: Consensus cryoEM map of CD20 in complex with wild type Rituximab Fab 手法: EM (単粒子) / 解像度: 2.5 Å EMDB-43214: Constituent map: Focused refinement of CD20 and Fab variable domain in complex of CD20 with Rituximab Fab 手法: EM (単粒子) / 解像度: 2.6 Å EMDB-43215: Constituent map: Focused refinement of CD20 in complex of CD20 with Rituximab Fab 手法: EM (単粒子) / 解像度: 2.5 Å 43216 8vgo EMDB-43216, PDB-8vgo: CryoEM structure of CD20 in complex with engineered conformationally rigid Rituximab.4DS Fab 手法: EM (単粒子) / 解像度: 2.6 Å EMDB-43217: Consensus cryoEM map of CD20 in complex with engineered conformationally rigid Rituximab.4DS Fab 手法: EM (単粒子) / 解像度: 2.6 Å EMDB-43218: Constituent map: Focused refinement of CD20 and Fab variable domains in complex of CD20 and Rituximab.4DS Fab 手法: EM (単粒子) / 解像度: 2.6 Å EMDB-43219: Constituent map: Focused refinement of CD20 in complex of CD20 with Rituximab.4DS Fab 手法: EM (単粒子) / 解像度: 2.7 Å 43220 8vgp EMDB-43220, PDB-8vgp: CryoEM structure of Angiopoietin-2 in complex with engineered conformationally rigid Fab 5A12.6DS 手法: EM (単粒子) / 解像度: 2.7 Å 43221 8vgq EMDB-43221, PDB-8vgq: CryoEM structure of GNE-1952-alkylated KRAS G12C in complex with engineered conformationally rigid Fab 2H11.4DS 手法: EM (単粒子) / 解像度: 2.8 Å PDB-8veg: Crystal structure of an engineered conformationally rigid anti-Tryptase Fab variant E104.v1.4DS.S112F 手法: X-RAY DIFFRACTION / 解像度: 2 Å PDB-8vge: Crystal structure of an engineered conformationally rigid anti-Tryptase Fab variant E104.v1.4DS.A114F 手法: X-RAY DIFFRACTION / 解像度: 2.01 Å PDB-8vgf: Crystal structure of an engineered conformationally rigid anti-Tryptase Fab variant E104.v1.5DS 手法: X-RAY DIFFRACTION / 解像度: 2.14 Å PDB-8vgg: Crystal structure of an engineered conformationally rigid anti-Tryptase Fab variant E104.v1.6DS 手法: X-RAY DIFFRACTION / 解像度: 2.71 Å
化合物	ChemComp-HOH: WATER ChemComp-CA: Unknown entry / カルシウムジカチオン PDB-1aaw: THE STRUCTURAL BASIS FOR THE ALTERED SUBSTRATE SPECIFICITY OF THE R292D ACTIVE SITE MUTANT OF ASPARTATE AMINOTRANSFERASE FROM E. COLI ChemComp-GDP: GUANOSINE-5'-DIPHOSPHATE / GDP / GDP, エネルギー貯蔵分子YM ChemComp-MG*: Unknown entry / マグネシウムジカチオン
由来	homo sapiens (ヒト) aliarcobacter butzleri rm4018 (バクテリア) mus musculus (ハツカネズミ)
キーワード	IMMUNE SYSTEM / antibody fragment / fab / protein engineering / tryptase / HYDROLASE/IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM complex / TRANSPORT PROTEIN / ion channel / MEMBRANE PROTEIN/IMMUNE SYSTEM / membrane protein / MEMBRANE PROTEIN-IMMUNE SYSTEM complex / CYTOKINE/IMMUNE SYSTEM / antigen binding fragment / CYTOKINE-IMMUNE SYSTEM complex / ONCOPROTEIN/IMMUNE SYSTEM / gtpase / ONCOPROTEIN-MMUNE SYSTEM complex / ONCOPROTEIN-IMMUNE SYSTEM complex