1TP7

Crystal Structure of the RNA-dependent RNA Polymerase from Human Rhinovirus 16

Summary for 1TP7

• Entry DOI: 10.2210/pdb1tp7/pdb
• Descriptor: Genome polyprotein, SULFATE ION, 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE, ... (4 entities in total)
• Functional Keywords: rhinovirus, rna, polymerase, 3d, transferase
• Biological source: Human rhinovirus 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: 4
• Total formula weight: 211893.52

Authors

Appleby, T.C.,Luecke, H.,Shim, J.H.,Wu, J.Z.,Cheney, I.W.,Zhong, W.,Vogeley, L.,Hong, Z.,Yao, N. (deposition date: 2004-06-15, release date: 2005-06-21, Last modification date: 2024-11-20)

Primary citation

Appleby, T.C.,Luecke, H.,Shim, J.H.,Wu, J.Z.,Cheney, I.W.,Zhong, W.,Vogeley, L.,Hong, Z.,Yao, N.
Crystal structure of complete rhinovirus RNA polymerase suggests front loading of protein primer.
J.Virol., 79:277-288, 2005

PubMed Abstract: Picornaviruses utilize virally encoded RNA polymerase and a uridylylated protein primer to ensure replication of the entire viral genome. The molecular details of this mechanism are not well understood due to the lack of structural information. We report the crystal structure of human rhinovirus 16 3D RNA-dependent RNA polymerase (HRV16 3Dpol) at a 2.4-A resolution, representing the first complete polymerase structure from the Picornaviridae family. HRV16 3Dpol shares the canonical features of other known polymerase structures and contains an N-terminal region that tethers the fingers and thumb subdomains, forming a completely encircled active site cavity which is accessible through a small tunnel on the backside of the molecule. The small thumb subdomain contributes to the formation of a large cleft on the front face of the polymerase which also leads to the active site. The cleft appears large enough to accommodate a template:primer duplex during RNA elongation or a protein primer during the uridylylation stage of replication initiation. Based on the structural features of HRV16 3Dpo1 and the catalytic mechanism known for all polymerases, a front-loading model for uridylylation is proposed.

PubMed: 15596823
DOI: 10.1128/JVI.79.1.277-288.2005

Experimental method

X-RAY DIFFRACTION (2.4 Å)