Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Disulfi de constrained Fabs overcome target size limitation for high-resolution single-particle cryo-EM.
Journal, issue, pages	bioRxiv, Year 2024
Publish date	May 13, 2024
Authors	Jennifer E Kung / Matthew C Johnson / Christine C Jao / Christopher P Arthur / Dimitry Tegunov / Alexis Rohou / Jawahar Sudhamsu /
PubMed Abstract	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.
External links	bioRxiv / PubMed:38798381 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2 - 2.9 Å
Structure data	43200 8vgh EMDB-43200, PDB-8vgh: CryoEM structure of tryptase in complex with wild type anti-tryptase Fab E104.v1 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 2.6 Å EMDB-43205: Consensus cryoEM map of Nav1.7 in complex with wild type Fab 7A9 Method: EM (single particle) / Resolution: 2.5 Å EMDB-43206: Constituent EM map: Focused refinement of Fab 7A9 in complex of Nav1.7 and Fab 7A9 Method: EM (single particle) / Resolution: 2.6 Å EMDB-43207: Constituent map: Focused refinement of Nav1.7 in complex of Nav1.7 and Fab 7A9 Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 2.6 Å EMDB-43209: Consensus cryoEM map of Nav1.7 in complex with engineered conformationally rigid Fab 7A9.4DS Method: EM (single particle) / Resolution: 2.6 Å EMDB-43210: Constituent map: Focused refinement of Fab 7A9.4DS in complex of Nav1.7 and Fab 7A9.4DS Method: EM (single particle) / Resolution: 2.5 Å EMDB-43211: Constituent map: Focused refinement of Nav1.7 in complex of Nav1.7 and Fab 7A9.4DS Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 2.5 Å EMDB-43213: Consensus cryoEM map of CD20 in complex with wild type Rituximab Fab Method: EM (single particle) / Resolution: 2.5 Å EMDB-43214: Constituent map: Focused refinement of CD20 and Fab variable domain in complex of CD20 with Rituximab Fab Method: EM (single particle) / Resolution: 2.6 Å EMDB-43215: Constituent map: Focused refinement of CD20 in complex of CD20 with Rituximab Fab Method: EM (single particle) / Resolution: 2.5 Å 43216 8vgo EMDB-43216, PDB-8vgo: CryoEM structure of CD20 in complex with engineered conformationally rigid Rituximab.4DS Fab Method: EM (single particle) / Resolution: 2.6 Å EMDB-43217: Consensus cryoEM map of CD20 in complex with engineered conformationally rigid Rituximab.4DS Fab Method: EM (single particle) / Resolution: 2.6 Å EMDB-43218: Constituent map: Focused refinement of CD20 and Fab variable domains in complex of CD20 and Rituximab.4DS Fab Method: EM (single particle) / Resolution: 2.6 Å EMDB-43219: Constituent map: Focused refinement of CD20 in complex of CD20 with Rituximab.4DS Fab Method: EM (single particle) / Resolution: 2.7 Å 43220 8vgp EMDB-43220, PDB-8vgp: CryoEM structure of Angiopoietin-2 in complex with engineered conformationally rigid Fab 5A12.6DS Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 2.8 Å PDB-8veg: Crystal structure of an engineered conformationally rigid anti-Tryptase Fab variant E104.v1.4DS.S112F Method: X-RAY DIFFRACTION / Resolution: 2 Å PDB-8vge: Crystal structure of an engineered conformationally rigid anti-Tryptase Fab variant E104.v1.4DS.A114F Method: X-RAY DIFFRACTION / Resolution: 2.01 Å PDB-8vgf: Crystal structure of an engineered conformationally rigid anti-Tryptase Fab variant E104.v1.5DS Method: X-RAY DIFFRACTION / Resolution: 2.14 Å PDB-8vgg: Crystal structure of an engineered conformationally rigid anti-Tryptase Fab variant E104.v1.6DS Method: X-RAY DIFFRACTION / Resolution: 2.71 Å
Chemicals	ChemComp-HOH: WATER ChemComp-CA: Unknown entry 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, energy-carrying moleculeYM ChemComp-MG*: Unknown entry
Source	homo sapiens (human) aliarcobacter butzleri rm4018 (bacteria) mus musculus (house mouse)
Keywords	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