The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability.
The crystal and molecular structure of an RNA duplex corresponding to the high affinity Rev protein binding element (RBE) has been determined at 2.1-A resolution. Four unique duplexes are present in the crystal, comprising two structural variants. In each duplex, the RNA double helix consists of an annealed 12-mer and 14-mer that form an asymmetric internal loop consisting of G-G and G-A noncanonical base pairs and a flipped-out uridine. The 12-mer strand has an A-form conformation, whereas the 14-mer strand is distorted to accommodate the bulges and noncanonical base pairing. In contrast to the NMR model of the unbound RBE, an asymmetric G-G pair with N2-N7 and N1-O6 hydrogen bonding, is formed in each helix. The G-A base pairing agrees with the NMR structure in one structural variant, but forms a novel water-mediated pair in the other. A backbone flip and reorientation of the G-G base pair is required to assume the RBE conformation present in the NMR model of the complex between the RBE and the Rev peptide.
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Macromolecular Crystallography Facility and Structural Biology Department, Melvin Calvin Building, Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.
Holbrook
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Holbrook
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D001483:Base Sequence; D018360:Crystallography, X-Ray; D015694:Gene Products, rev / Q000737:chemistry* / Q000378:metabolism; D015497:HIV-1 / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009687:Nuclear Proteins / Q000737:chemistry* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D054321:rev Gene Products, Human Immunodeficiency Virus
D015694:Gene Products, rev; D009687:Nuclear Proteins; D009843:Oligoribonucleotides; D012367:RNA, Viral; C069802:nuclear factor, RRE binding; D054321:rev Gene Products, Human Immunodeficiency Virus