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	Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting.
Journal, issue, pages	Nat Methods, Vol. 20, Issue 9, Page 1400-1408, Year 2023
Publish date	Aug 17, 2023
Authors	Stefania Torino / Mugdha Dhurandhar / Annelore Stroobants / Raf Claessens / Rouslan G Efremov /
PubMed Abstract	Single-particle cryogenic electron microscopy (cryo-EM) allows reconstruction of high-resolution structures of proteins in different conformations. Protein function often involves transient ...Single-particle cryogenic electron microscopy (cryo-EM) allows reconstruction of high-resolution structures of proteins in different conformations. Protein function often involves transient functional conformations, which can be resolved using time-resolved cryo-EM (trEM). In trEM, reactions are arrested after a defined delay time by rapid vitrification of protein solution on the EM grid. Despite the increasing interest in trEM among the cryo-EM community, making trEM samples with a time resolution below 100 ms remains challenging. Here we report the design and the realization of a time-resolved cryo-plunger that combines a droplet-based microfluidic mixer with a laser-induced generator of microjets that allows rapid reaction initiation and plunge-freezing of cryo-EM grids. Using this approach, a time resolution of 5 ms was achieved and the protein density map was reconstructed to a resolution of 2.1 Å. trEM experiments on GroEL:GroES chaperonin complex resolved the kinetics of the complex formation and visualized putative short-lived conformations of GroEL-ATP complex.
External links	Nat Methods / PubMed:37592181
Methods	EM (single particle)
Resolution	2.1 - 7.1 Å
Structure data	16091 8bk7 EMDB-16091, PDB-8bk7: Cryo-EM structure of beta-galactosidase at 3.3 A resolution plunged 5 ms after mixing with apoferritin Method: EM (single particle) / Resolution: 3.3 Å 16092 8bk8 EMDB-16092, PDB-8bk8: Cryo-EM structure of beta-galactosidase at 2.9 A resolution plunged 205 ms after mixing with apoferritin Method: EM (single particle) / Resolution: 2.9 Å 16093 8bk9 EMDB-16093, PDB-8bk9: Cryo-EM structure of mouse heavy-chain apoferritin at 2.1 A plunged 5ms after mixing with b-galactosidase Method: EM (single particle) / Resolution: 2.1 Å 16094 8bka EMDB-16094, PDB-8bka: Cryo-EM structure of mouse heavy-chain apoferritin at 2.7 A plunged 35ms after mixing with b-galactosidase Method: EM (single particle) / Resolution: 2.7 Å 16095 8bkb EMDB-16095, PDB-8bkb: Cryo-EM structure of mouse heavy-chain apoferritin at 2.2 A plunged 205ms after mixing with b-galactosidase Method: EM (single particle) / Resolution: 2.2 Å 16097 8bkg EMDB-16097, PDB-8bkg: Cryo-EM structure of beta-galactosidase at 3.2 A resolution plunged 35 ms after mixing with apoferritin Method: EM (single particle) / Resolution: 3.2 Å 16099 8bkz EMDB-16099: GroEL:GroES-ATP complex under continuous turnover condirions PDB-8bkz: GroEL:GroES-ATP complex under continuous turnover conditions Method: EM (single particle) / Resolution: 2.3 Å 16100 8bl2 EMDB-16100, PDB-8bl2: Structure of GroEL-ATP complex plunge frozen 200 ms after reaction initiation Method: EM (single particle) / Resolution: 2.3 Å 16102 8bl7 EMDB-16102, PDB-8bl7: Structure of GroEL-nucleotide complex in ADP-like conformation plunged 13 ms after mixing with ATP Method: EM (single particle) / Resolution: 4.4 Å 16106 8blc EMDB-16106, PDB-8blc: Structure of the GroEL-ATP complex plunge-frozen 50 ms after mixing with ATP Method: EM (single particle) / Resolution: 2.7 Å 16107 8bld EMDB-16107, PDB-8bld: Structure of the GroEL(ATP7/ADP7) complex plunged 13 ms after mixing with ATP Method: EM (single particle) / Resolution: 4.4 Å 16108 8ble EMDB-16108, PDB-8ble: Structure of GroEL-nucleotide complex in ADP-like conformation plunged 50 ms after mixing with ATP Method: EM (single particle) / Resolution: 4.0 Å 16109 8blf EMDB-16109, PDB-8blf: Structure of the GroEL(ATP7/ADP7) complex plunged 50 ms after mixing with ATP Method: EM (single particle) / Resolution: 3.9 Å 16115 8bly EMDB-16115, PDB-8bly: Structure of the GroEL-ATP complex plunge-frozen 13 ms after mixing with ATP Method: EM (single particle) / Resolution: 3.2 Å 16116 8bm0 EMDB-16116, PDB-8bm0: Structure of GroEL:GroES-ATP complex plunge frozen 200 ms after reaction initiation Method: EM (single particle) / Resolution: 3.4 Å 16117 8bm1 EMDB-16117, PDB-8bm1: Structure of GroEL:GroES-ATP complex under continuous turnover conditions Method: EM (single particle) / Resolution: 2.7 Å 16118 8bmd EMDB-16118, PDB-8bmd: Structure of GroEL-ATP complex under continuous turnover conditions Method: EM (single particle) / Resolution: 2.8 Å 16119 8bmo EMDB-16119, PDB-8bmo: Structure of GroEL:GroES complex exhibiting ADP-conformation in trans ring obtained under the continuous turnover conditions Method: EM (single particle) / Resolution: 3.4 Å 16125 8bmt EMDB-16125, PDB-8bmt: Structure of GroEL:GroES-ATP complex plunge frozen 200 ms after reaction initiation Method: EM (single particle) / Resolution: 2.5 Å EMDB-16154: Map of the GroEL-ES-ATP complex plunge-frozen 50 ms after mixing with ATP Method: EM (single particle) / Resolution: 7.1 Å EMDB-16157: Map of GroEL:GroES-(ADP) complex plunge frozen 200 ms after reaction initiation with ATP Method: EM (single particle) / Resolution: 6.3 Å
Chemicals	ChemComp-FE: Unknown entry / Iron ChemComp-HOH: WATER / Water ChemComp-MG: Unknown entry ChemComp-K: Unknown entry ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate
Source	escherichia coli (E. coli) escherichia coli k-12 (bacteria) mus musculus (house mouse)
Keywords	HYDROLASE / Glycosyl hydrolase / METAL BINDING PROTEIN / iron storage / ferritin / octahedral / CHAPERONE / GroEL / GroES