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
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Journal
IF	>30 >20 >10 >5 all

Title	Structural basis for transthiolation intermediates in the ubiquitin pathway.
Journal, issue, pages	Nature, Vol. 633, Issue 8028, Page 216-223, Year 2024
Publish date	Aug 14, 2024
Authors	Tomasz Kochańczyk / Zachary S Hann / Michaelyn C Lux / Avelyn Mae V Delos Reyes / Cheng Ji / Derek S Tan / Christopher D Lima /
PubMed Abstract	Transthiolation (also known as transthioesterification) reactions are used in the biosynthesis of acetyl coenzyme A, fatty acids and polyketides, and for post-translational modification by ubiquitin ...Transthiolation (also known as transthioesterification) reactions are used in the biosynthesis of acetyl coenzyme A, fatty acids and polyketides, and for post-translational modification by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. For the Ub pathway, E1 enzymes catalyse transthiolation from an E1~Ub thioester to an E2~Ub thioester. Transthiolation is also required for transfer of Ub from an E2~Ub thioester to HECT (homologous to E6AP C terminus) and RBR (ring-between-ring) E3 ligases to form E3~Ub thioesters. How isoenergetic transfer of thioester bonds is driven forward by enzymes in the Ub pathway remains unclear. Here we isolate mimics of transient transthiolation intermediates for E1-Ub(T)-E2 and E2-Ub(T)-E3 complexes (where T denotes Ub in a thioester or Ub undergoing transthiolation) using a chemical strategy with native enzymes and near-native Ub to capture and visualize a continuum of structures determined by single-particle cryo-electron microscopy. These structures and accompanying biochemical experiments illuminate conformational changes in Ub, E1, E2 and E3 that are coordinated with the chemical reactions to facilitate directional transfer of Ub from each enzyme to the next.
External links	Nature / PubMed:39143218 / PubMed Central
Methods	EM (single particle)
Resolution	2.5 - 4.16 Å
Structure data	44200 9b55 EMDB-44200, PDB-9b55: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 1 Method: EM (single particle) / Resolution: 3.23 Å 44201 9b56 EMDB-44201, PDB-9b56: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 2 Method: EM (single particle) / Resolution: 3.35 Å 44202 9b57 EMDB-44202, PDB-9b57: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 3 Method: EM (single particle) / Resolution: 3.37 Å 44203 9b58 EMDB-44203, PDB-9b58: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 4 Method: EM (single particle) / Resolution: 3.39 Å 44204 9b59 EMDB-44204, PDB-9b59: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 5 Method: EM (single particle) / Resolution: 3.49 Å 44205 9b5a EMDB-44205, PDB-9b5a: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 6 Method: EM (single particle) / Resolution: 3.65 Å 44206 9b5b EMDB-44206, PDB-9b5b: Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 7 Method: EM (single particle) / Resolution: 3.31 Å 44207 9b5c EMDB-44207, PDB-9b5c: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - consensus map and model Method: EM (single particle) / Resolution: 2.5 Å 44208 9b5d EMDB-44208, PDB-9b5d: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 1 map and model from consensus Method: EM (single particle) / Resolution: 2.8 Å 44209 9b5e EMDB-44209, PDB-9b5e: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from consensus Method: EM (single particle) / Resolution: 2.81 Å 44210 9b5f EMDB-44210, PDB-9b5f: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 1 map and model (Ub(A)/ATP/Mg) Method: EM (single particle) / Resolution: 2.78 Å 44211 9b5g EMDB-44211, PDB-9b5g: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 2 map and model (Ub(A)/ATP/Mg) Method: EM (single particle) / Resolution: 2.67 Å 44212 9b5h EMDB-44212, PDB-9b5h: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 3 map and model (Ub(A)-AMP/PPi/Mg) Method: EM (single particle) / Resolution: 2.69 Å 44213 9b5i EMDB-44213, PDB-9b5i: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 4 map and model (Ub(A)-AMP/PPi/Mg) Method: EM (single particle) / Resolution: 2.7 Å 44214 9b5j EMDB-44214, PDB-9b5j: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 5 map and model (Ub(A)-AMP) Method: EM (single particle) / Resolution: 2.86 Å 44215 9b5k EMDB-44215, PDB-9b5k: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 1 map and model from cluster 1 (Ub(A)/ATP/Mg) Method: EM (single particle) / Resolution: 3.16 Å 44216 9b5l EMDB-44216, PDB-9b5l: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from cluster 5 (Ub(A)-AMP) Method: EM (single particle) / Resolution: 3.3 Å 44217 9b5m EMDB-44217, PDB-9b5m: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - consensus map and model Method: EM (single particle) / Resolution: 2.79 Å 44218 9b5n EMDB-44218, PDB-9b5n: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from consensus Method: EM (single particle) / Resolution: 3.12 Å 44219 9b5o EMDB-44219, PDB-9b5o: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 10 map and model from consensus Method: EM (single particle) / Resolution: 3.19 Å 44220 9b5p EMDB-44220, PDB-9b5p: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 1 map and model (ATP/Mg) Method: EM (single particle) / Resolution: 3.08 Å 44221 9b5q EMDB-44221, PDB-9b5q: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 2 map and model (ATP/Mg) Method: EM (single particle) / Resolution: 2.95 Å 44222 9b5r EMDB-44222, PDB-9b5r: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 3 map and model (ATP/Mg) Method: EM (single particle) / Resolution: 2.95 Å 44223 9b5s EMDB-44223, PDB-9b5s: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 4 map and model (ATP/Mg) Method: EM (single particle) / Resolution: 2.96 Å 44224 9b5t EMDB-44224, PDB-9b5t: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 5 map and model (ATP/Mg) Method: EM (single particle) / Resolution: 3.16 Å 44225 9b5u EMDB-44225, PDB-9b5u: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from cluster 1 (ATP/Mg) Method: EM (single particle) / Resolution: 3.67 Å 44226 9b5v EMDB-44226, PDB-9b5v: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 10 map and model from cluster 1 (ATP/Mg) Method: EM (single particle) / Resolution: 3.94 Å 44227 9b5w EMDB-44227, PDB-9b5w: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from cluster 5 (ATP/Mg) Method: EM (single particle) / Resolution: 3.96 Å 44228 9b5x EMDB-44228, PDB-9b5x: Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 10 map and model from cluster 5 (ATP/Mg) Method: EM (single particle) / Resolution: 4.16 Å
Chemicals	PDB-1aiv: APO OVOTRANSFERRIN ChemComp-MG: Unknown entry ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-POP: PYROPHOSPHATE 2- ChemComp-AMP: ADENOSINE MONOPHOSPHATE / AMPYM
Source	schizosaccharomyces pombe 972h- (yeast)
Keywords	LIGASE / UBIQUITIN / E2 / E3 / HECT / NEDD4 / RSP5 / PUB2 / UBC4 / TRANSTHIOESTERIFICATION / THIOESTER / TRANSTHIOLATION / TETRAHEDRAL INTERMEDIATE / ADENYLATION / INHIBITOR / NUCLEUS / PHOSPHOPROTEIN / UBL CONJUGATION PATHWAY / UBL / ATP ATP-BINDING / AMP / NUCLEOTIDE-BINDING / ISOPEPTIDE BOND / E1 / UBA1 / ATP / ATP-binding