9YKE

GroEL Apoenzyme

Summary for 9YKE

• Entry DOI: 10.2210/pdb9yke/pdb
• Related: 9C0C
• EMDB information: 73045
• Descriptor: Chaperonin GroEL (1 entity in total)
• Functional Keywords: chaperone, tetradecamer, nucleotide binding, apoenzyme
• Biological source: Escherichia coli
• Total number of polymer chains: 14
• Total formula weight: 774889.99

Authors

Zafar, H.,Glass, K.C.,Malone, K.L. (deposition date: 2025-10-07, release date: 2025-12-10, Last modification date: 2026-03-18)

Primary citation

Zafar, H.,Malone, K.L.,Singh, A.K.,Cianfrocco, M.A.,Glass, K.C.
Breaking barriers: transitioning from X-ray crystallography to cryo-EM for structural studies.
Acta Crystallogr D Struct Biol, 82:253-273, 2026

PubMed Abstract: Cryo-electron microscopy (cryo-EM) has transformed structural biology by enabling near-atomic resolution of large macromolecular complexes without the need for crystallization. Here, we describe our laboratory's transition from X-ray crystallography to single-particle cryo-EM to investigate the ATPase family AAA+ domain-containing protein 2B (ATAD2B), a chromatin regulator implicated in epigenetic signaling. We outline the challenges encountered during protein expression, purification and sample preparation, including co-purification of the chaperonin GroEL, and the strategies employed to overcome these obstacles. Our workflow highlights critical steps in sample optimization, grid vitrification and data processing using CryoSPARC, cisTEM and Topaz, as well as computational requirements for high-resolution reconstructions. We also discuss model-building, refinement and validation approaches, emphasizing best practices for new cryo-EM users. This work provides practical insights for structural biologists adopting cryo-EM, particularly for large, flexible protein complexes, and underscores the importance of integrated approaches combining biochemical, computational and imaging strategies.

PubMed: 41709867
DOI: 10.1107/S205979832600080X

Experimental method

ELECTRON MICROSCOPY (3.7 Å)