6JXM

Crystal Structure of phi29 pRNA domain II

Summary for 6JXM

• Entry DOI: 10.2210/pdb6jxm/pdb
• Descriptor: RNA (97-mer), MAGNESIUM ION, BARIUM ION (3 entities in total)
• Functional Keywords: phi29 bacteriophage, rna
• Biological source: Bacillus virus phi29
• Total number of polymer chains: 1
• Total formula weight: 33607.69

Authors

Cai, R.,Price, I.R.,Ding, F.,Wu, F.,Chen, T.,Zhang, Y.,Liu, G.,Jardine, P.J.,Lu, C.,Ke, A. (deposition date: 2019-04-24, release date: 2019-08-21, Last modification date: 2023-11-22)

Primary citation

Cai, R.,Price, I.R.,Ding, F.,Wu, F.,Chen, T.,Zhang, Y.,Liu, G.,Jardine, P.J.,Lu, C.,Ke, A.
ATP/ADP modulates gp16-pRNA conformational change in the Phi29 DNA packaging motor.
Nucleic Acids Res., 47:9818-9828, 2019

PubMed Abstract: Packaging of phage phi29 genome requires the ATPase gp16 and prohead RNA (pRNA). The highly conserved pRNA forms the interface between the connector complex and gp16. Understanding how pRNA interacts with gp16 under packaging conditions can shed light on the molecular mechanism of the packaging motor. Here, we present 3D models of the pRNA-gp16 complex and its conformation change in response to ATP or ADP binding. Using a combination of crystallography, small angle X-ray scattering and chemical probing, we find that the pRNA and gp16 forms a 'Z'-shaped complex, with gp16 specifically binds to pRNA domain II. The whole complex closes in the presence of ATP, and pRNA domain II rotates open as ATP hydrolyzes, before resetting after ADP is released. Our results suggest that pRNA domain II actively participates in the packaging process.

PubMed: 31396619
DOI: 10.1093/nar/gkz692

Experimental method

X-RAY DIFFRACTION (3.32 Å)