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	Visualizing chaperonin function in situ by cryo-electron tomography.
Journal, issue, pages	Nature, Vol. 633, Issue 8029, Page 459-464, Year 2024
Publish date	Aug 21, 2024
Authors	Jonathan Wagner / Alonso I Carvajal / Andreas Bracher / Florian Beck / William Wan / Stefan Bohn / Roman Körner / Wolfgang Baumeister / Ruben Fernandez-Busnadiego / F Ulrich Hartl /
PubMed Abstract	Chaperonins are large barrel-shaped complexes that mediate ATP-dependent protein folding. The bacterial chaperonin GroEL forms juxtaposed rings that bind unfolded protein and the lid-shaped cofactor ...Chaperonins are large barrel-shaped complexes that mediate ATP-dependent protein folding. The bacterial chaperonin GroEL forms juxtaposed rings that bind unfolded protein and the lid-shaped cofactor GroES at their apertures. In vitro analyses of the chaperonin reaction have shown that substrate protein folds, unimpaired by aggregation, while transiently encapsulated in the GroEL central cavity by GroES. To determine the functional stoichiometry of GroEL, GroES and client protein in situ, here we visualized chaperonin complexes in their natural cellular environment using cryo-electron tomography. We find that, under various growth conditions, around 55-70% of GroEL binds GroES asymmetrically on one ring, with the remainder populating symmetrical complexes. Bound substrate protein is detected on the free ring of the asymmetrical complex, defining the substrate acceptor state. In situ analysis of GroEL-GroES chambers, validated by high-resolution structures obtained in vitro, showed the presence of encapsulated substrate protein in a folded state before release into the cytosol. Based on a comprehensive quantification and conformational analysis of chaperonin complexes, we propose a GroEL-GroES reaction cycle that consists of linked asymmetrical and symmetrical subreactions mediating protein folding. Our findings illuminate the native conformational and functional chaperonin cycle directly within cells.
External links	Nature / PubMed:39169181 / PubMed Central
Methods	EM (single particle) / EM (subtomogram averaging)
Resolution	2.5 - 15.2 Å
Structure data	17418 8p4m EMDB-17418, PDB-8p4m: CryoEM structure of a C7-symmetrical GroEL7-GroES7 cage in presence of ADP-BeFx Method: EM (single particle) / Resolution: 2.5 Å 17420 8p4n EMDB-17420, PDB-8p4n: CryoEM structure of a GroEL7-GroES7 cage with encapsulated disordered substrate MetK in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 2.9 Å 17421 8p4o EMDB-17421, PDB-8p4o: CryoEM structure of a GroEL7-GroES7 cage with encapsulated ordered substrate MetK in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 3.04 Å EMDB-17422: Density for MetK encapsulated in the GroEL7-GroES7 cage Method: EM (single particle) / Resolution: 3.7 Å EMDB-17423: Symmetry-averaged GroEL7-GroES7 chamber with encapsulated disordered substrate MetK obtained by in vitro cryo electron tomography Method: EM (subtomogram averaging) / Resolution: 7.6 Å EMDB-17424: Symmetry-averaged GroEL7-GroES7 chamber with encapsulated ordered substrate MetK obtained by in vitro cryo electron tomography Method: EM (subtomogram averaging) / Resolution: 8.0 Å 17425 8p4p EMDB-17425, PDB-8p4p: Structure average of GroEL14 complexes found in the cytosol of Escherichia coli overexpressing GroEL obtained by cryo electron tomography Method: EM (subtomogram averaging) / Resolution: 9.6 Å 17426 8p4r EMDB-17426, PDB-8p4r: In situ structure average of GroEL14-GroES14 complexes in Escherichia coli cytosol obtained by cryo electron tomography Method: EM (subtomogram averaging) / Resolution: 11.9 Å EMDB-17534: Cryo-EM structure of a D7-symmetrical GroEL14-GroES14 complex in presence of ADP-BeFx Method: EM (single particle) / Resolution: 2.74 Å EMDB-17535: Cryo-EM structure of a C7-symmetrical GroEL14-GroES7 complex in presence of ADP-BeFx Method: EM (single particle) / Resolution: 2.66 Å EMDB-17559: In situ structure average of GroEL7-GroES7 chamber with no or disordered substrate in Escherichia coli cytosol obtained by cryo electron tomography Method: EM (subtomogram averaging) / Resolution: 15.1 Å EMDB-17560: In situ structure average of GroEL7-GroES7 chamber with encapsulated, ordered substrate in Escherichia coli cytosol obtained by cryo electron tomography Method: EM (subtomogram averaging) / Resolution: 15.2 Å EMDB-17561: Cryo-ET subtomogram of 70S ribosomes in Escherichia coli cells at 37 and 46 degrees centigrade and in Escherichia coli cells overexpressing GroELS and MetK Method: EM (subtomogram averaging) / Resolution: 8.4 Å EMDB-17562: Cryo-ET subtomogram of 70S ribosomes in Escherichia coli cells overexpressing GroEL Method: EM (subtomogram averaging) / Resolution: 6.3 Å EMDB-17563: CryoEM structure of a GroEL14-GroES7 cage with encapsulated ordered substrate MetK in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 3.47 Å EMDB-17564: CryoEM structure of a GroEL14-GroES7 cage with encapsulated disordered substrate MetK in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 3.22 Å EMDB-17565: CryoEM structure of a GroEL14-GroES14 cage with two encapsulated disordered MetK substrates in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 3.22 Å EMDB-17566: CryoEM structure of a (GroEL)14-(GroES)14 complex with encapsulated ordered MetK substrate in one chamber and no or disordered MetK substrate in the other chamber in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 3.15 Å EMDB-17567: Conformer 1 of the (GroEL)14(GroES)14 complex with two encapsulated, ordered and near-native MetK substrate molecules in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 4.5 Å EMDB-17568: Conformer 2 of the (GroEL)14(GroES)14 complex with two encapsulated, near-native and ordered MetK substrates in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 4.4 Å EMDB-17569: Conformer 3 of the (GroEL)14(GroES)14 complex with two encapsulated, near-native and ordered MetK substrates in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 4.4 Å EMDB-17570: Conformer 4 of the (GroEL)14(GroES)14 complex with two encapsulated, near-native and ordered MetK substrates in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 4.4 Å EMDB-17571: Conformer 5 of the (GroEL)14(GroES)14 complex with two encapsulated, near-native and ordered MetK substrates in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 4.7 Å EMDB-17572: Conformer 6 of the (GroEL)14(GroES)14 complex with two encapsulated, near-native and ordered MetK substrates in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 4.4 Å EMDB-17573: Conformer 7 of the (GroEL)14(GroES)14 complex with two encapsulated, near-native and ordered MetK substrates in the presence of ADP-BeFx Method: EM (single particle) / Resolution: 4.4 Å 18735 8qxs EMDB-18735, PDB-8qxs: CryoEM structure of a GroEL14-GroES7 complex in presence of ADP-BeFx with wide GroEL7 trans ring conformation Method: EM (single particle) / Resolution: 3.12 Å 18736 8qxt EMDB-18736, PDB-8qxt: CryoEM structure of a GroEL14-GroES7 complex in presence of ADP-BeFx with narrow GroEL7 trans ring conformation Method: EM (single particle) / Resolution: 2.9 Å 18737 8qxu EMDB-18737, PDB-8qxu: In situ structure average of GroEL14-GroES7 complexes with wide GroEL7 trans ring conformation in Escherichia coli cytosol obtained by cryo electron tomography Method: EM (subtomogram averaging) / Resolution: 12.0 Å 18738 8qxv EMDB-18738, PDB-8qxv: In situ structure average of GroEL14-GroES7 complexes with narrow GroEL7 trans ring conformation in Escherichia coli cytosol obtained by cryo electron tomography Method: EM (subtomogram averaging) / Resolution: 13.6 Å
Chemicals	ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-BEF: BERYLLIUM TRIFLUORIDE ION ChemComp-K: Unknown entry ChemComp-HOH: WATER ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM
Source	escherichia coli (E. coli) escherichia coli bl21(de3) (bacteria)
Keywords	CHAPERONE / Chaperonin / Folding cage / proteostasis / heat shock / ATPase