9V1N

CTP synthase RXN-condition state 2

Summary for 9V1N

• Entry DOI: 10.2210/pdb9v1n/pdb
• EMDB information: 64699
• Descriptor: CTP synthase, ADENOSINE-5'-DIPHOSPHATE, [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate, ... (4 entities in total)
• Functional Keywords: ctp synthase, ctps, ligase
• Biological source: Drosophila melanogaster (fruit fly)
• Total number of polymer chains: 3
• Total formula weight: 188396.21

Authors

Guo, C.J. (deposition date: 2025-05-19, release date: 2026-10-28)

Primary citation

Guo, C.J.,Wu, Y.F.,Guo, S.Y.,Fu, Y.,Wang, W.,Liu, J.L.
Reaction-based cryo-EM resolves the continuous conformational spectrum of CTP synthase catalysis.
Proc.Natl.Acad.Sci.USA, 123:e2620271123-e2620271123, 2026

PubMed Abstract: Capturing enzymes under native turnover conditions remains a grand challenge in structural biology. Here, we develop a reaction-based cryo-electron microscopy (cryo-EM) strategy that directly samples cytidine triphosphate synthase (CTPS) from actively catalyzing mixtures containing only natural substrates and allosteric effectors. By integrating reaction-based sampling with three-dimensional variability analysis, we resolve a continuous conformational spectrum of CTPS during catalysis. This approach visualizes the chemical progression of 4-phosphoryl-uridine triphosphate (4Pi-UTP) formation and reveals a previously unobserved co-occupancy pattern of adenosine triphosphate (ATP) and CTP at the reaction end point. Cross-validation with nonhydrolyzable ATP analogs demonstrates that UTP phosphorylation by ATP, rather than mere ATP binding, shifts the conformational ensemble toward more closed states. Our findings establish reaction-based cryo-EM as a framework for resolving chemically annotated conformational ensembles without predefining a single trapped intermediate.

PubMed: 42853686
DOI: 10.1073/pnas.2620271123

Experimental method

ELECTRON MICROSCOPY (3.05 Å)