9YKC
Cryo-EM structure of GroEL-gammaATP
Summary for 9YKC
| Entry DOI | 10.2210/pdb9ykc/pdb |
| Related | 8bl7 9c0c |
| EMDB information | 73044 |
| Descriptor | Chaperonin GroEL, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER (2 entities in total) |
| Functional Keywords | chaperonin, tetradecamer, nucleotide-binding, allosteric-change, chaperone |
| Biological source | Escherichia coli |
| Total number of polymer chains | 14 |
| Total formula weight | 782215.45 |
| Authors | |
| 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 of ATAD2B. Biorxiv, 2025 Cited by 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 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: 41279824DOI: 10.1101/2025.10.13.682238 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.3 Å) |
Structure validation
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