4L3B
X-ray structure of the HRV2 A particle uncoating intermediate
Summary for 4L3B
| Entry DOI | 10.2210/pdb4l3b/pdb |
| Related | 1FPN 3TN9 |
| Descriptor | Protein VP1, Protein VP2, Protein VP3 (3 entities in total) |
| Functional Keywords | hrv2 capsid, virus |
| Biological source | Human rhinovirus A2 (HRV-2) More |
| Cellular location | Capsid protein VP0: Virion . Capsid protein VP4: Virion . Capsid protein VP2: Virion . Capsid protein VP3: Virion . Capsid protein VP1: Virion . Protein 2B: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side . Protein 2C: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side . Protein 3A: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side . Protein 3AB: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side . Viral protein genome-linked: Virion . Protease 3C: Host cytoplasm . Protein 3CD: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side . RNA-directed RNA polymerase: Host cytoplasmic vesicle membrane ; Peripheral membrane protein ; Cytoplasmic side : P04936 P04936 P04936 |
| Total number of polymer chains | 3 |
| Total formula weight | 88042.18 |
| Authors | Vives-Adrian, L.,Querol-Audi, J.,Garriga, D.,Pous, J.,Verdaguer, N. (deposition date: 2013-06-05, release date: 2013-11-27, Last modification date: 2024-10-30) |
| Primary citation | Pickl-Herk, A.,Luque, D.,Vives-Adrian, L.,Querol-Audi, J.,Garriga, D.,Trus, B.L.,Verdaguer, N.,Blaas, D.,Caston, J.R. Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle. Proc.Natl.Acad.Sci.USA, 110:20063-20068, 2013 Cited by PubMed Abstract: During infection, viruses undergo conformational changes that lead to delivery of their genome into host cytosol. In human rhinovirus A2, this conversion is triggered by exposure to acid pH in the endosome. The first subviral intermediate, the A-particle, is expanded and has lost the internal viral protein 4 (VP4), but retains its RNA genome. The nucleic acid is subsequently released, presumably through one of the large pores that open at the icosahedral twofold axes, and is transferred along a conduit in the endosomal membrane; the remaining empty capsids, termed B-particles, are shuttled to lysosomes for degradation. Previous structural analyses revealed important differences between the native protein shell and the empty capsid. Nonetheless, little is known of A-particle architecture or conformation of the RNA core. Using 3D cryo-electron microscopy and X-ray crystallography, we found notable changes in RNA-protein contacts during conversion of native virus into the A-particle uncoating intermediate. In the native virion, we confirmed interaction of nucleotide(s) with Trp(38) of VP2 and identified additional contacts with the VP1 N terminus. Study of A-particle structure showed that the VP2 contact is maintained, that VP1 interactions are lost after exit of the VP1 N-terminal extension, and that the RNA also interacts with residues of the VP3 N terminus at the fivefold axis. These associations lead to formation of a well-ordered RNA layer beneath the protein shell, suggesting that these interactions guide ordered RNA egress. PubMed: 24277846DOI: 10.1073/pnas.1312128110 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (6.5 Å) |
Structure validation
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