4K50

Rhinovirus 16 polymerase elongation complex (r1_form)

Summary for 4K50

• Entry DOI: 10.2210/pdb4k50/pdb
• Related: 3OL6 4K4S 4K4T 4K4U 4K4V 4K4W 4K4X 4K4Y 4K4Z
• Descriptor: RNA polymerase 3D-POL, RNA (33-MER), RNA (5'-R(P*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3'), ... (7 entities in total)
• Functional Keywords: polymerase, rna-dependent rna polymerase, protein-rna complex, transferase-rna complex, transferase/rna
• Biological source: Human rhinovirus A16 (HRV-16)
• Cellular location: Protein VP2: Virion. Protein VP3: Virion. Protein VP1: Virion. Protein 2B: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 2C: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 3A: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Protein 3B: Virion (Potential). Picornain 3C: Host cytoplasm (Potential). RNA-directed RNA polymerase 3D-POL: Host cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential): Q82122
• Total number of polymer chains: 12
• Total formula weight: 274437.85

Authors

Gong, P.,Peersen, O.B. (deposition date: 2013-04-12, release date: 2013-05-22, Last modification date: 2024-02-28)

Primary citation

Gong, P.,Kortus, M.G.,Nix, J.C.,Davis, R.E.,Peersen, O.B.
Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts.
Plos One, 8:e60272-e60272, 2013

PubMed Abstract: RNA-dependent RNA polymerases play a vital role in the growth of RNA viruses where they are responsible for genome replication, but do so with rather low fidelity that allows for the rapid adaptation to different host cell environments. These polymerases are also a target for antiviral drug development. However, both drug discovery efforts and our understanding of fidelity determinants have been hampered by a lack of detailed structural information about functional polymerase-RNA complexes and the structural changes that take place during the elongation cycle. Many of the molecular details associated with nucleotide selection and catalysis were revealed in our recent structure of the poliovirus polymerase-RNA complex solved by first purifying and then crystallizing stalled elongation complexes. In the work presented here we extend that basic methodology to determine nine new structures of poliovirus, coxsackievirus, and rhinovirus elongation complexes at 2.2-2.9 Å resolution. The structures highlight conserved features of picornaviral polymerases and the interactions they make with the template and product RNA strands, including a tight grip on eight basepairs of the nascent duplex, a fully pre-positioned templating nucleotide, and a conserved binding pocket for the +2 position template strand base. At the active site we see a pre-bound magnesium ion and there is conservation of a non-standard backbone conformation of the template strand in an interaction that may aid in triggering RNA translocation via contact with the conserved polymerase motif B. Moreover, by engineering plasticity into RNA-RNA contacts, we obtain crystal forms that are capable of multiple rounds of in-crystal catalysis and RNA translocation. Together, the data demonstrate that engineering flexible RNA contacts to promote crystal lattice formation is a versatile platform that can be used to solve the structures of viral RdRP elongation complexes and their catalytic cycle intermediates.

PubMed: 23667424
DOI: 10.1371/journal.pone.0060272

Experimental method

X-RAY DIFFRACTION (2.93 Å)