Structure of the Hepatitis C Virus IRES Bound to the Human 80S Ribosome: Remodeling of the HCV IRES

Boehringer, Daniel; Thermann, Rolf; Ostareck-Lederer, Antje; Lewis, Joe; Stark, Holger

doi:10.1016/j.str.2005.08.008

Cited by 163 publications

(255 citation statements)

References 50 publications

(93 reference statements)

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“…This suggests that the isolated IRES molecule undergoes motions that mainly correspond to the first PC. Upon binding to its cellular partners, the conformational flexibility of the IRES seems to be significantly reduced leading to the visualization of the molecule in the cryo-EM reconstructions of the different complexes, although the shape and width of the electron density suggest that the IRES RNA conserves some flexibility in its bound state 27,28 (Fig. 7c).…”

Section: Discussionmentioning

confidence: 99%

“…7a). In particular, motions along the second PC may take place in order to correctly position domain II within the tRNA exit (E) site and the mRNA binding cleft of the ribosome and to trigger conformational changes in the 40S subunit and in the IRES 26,28,46,47 (Fig. 7a).…”

Section: Discussionmentioning

confidence: 99%

“…To date, the only structural information available about the architecture of the entire IRES molecule comes from cryoelectron microscopy (cryo-EM) reconstructions of the IRES in complexes with cellular partners [26][27][28] . In these low-resolution structures, the HCV IRES adopts similar elongated conformations [26][27][28] .…”

mentioning

confidence: 99%

“…In these low-resolution structures, the HCV IRES adopts similar elongated conformations [26][27][28] . Upon formation of the 48S IRESpreinitiation complex, the basal part of domain III binds to the solvent-exposed side of the ribosomal 40S subunit, whereas the apical part binds to eIF3 9,12,26 ( Supplementary Fig.…”

mentioning

confidence: 99%

“…Previous biochemical studies and structural characterizations of different RNA fragments suggest that the free HCV IRES is an articulated molecule in which long structured parts are linked by flexible joints 16,18,28 . Here we built structural models of the entire isolated HCV IRES molecule and characterized its dynamics by SAXS, biomolecular simulations and computational tools.…”

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confidence: 99%

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Structure of the full-length HCV IRES in solution

et al. 2013

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The 5 0 -untranslated region of the hepatitis C virus genome contains an internal ribosome entry site (IRES) that initiates cap-independent translation of the viral RNA. Until now, the structural characterization of the entire (IRES) remained limited to cryo-electron microscopy reconstructions of the (IRES) bound to different cellular partners. Here we report an atomic model of free full-length hepatitis C virus (IRES) refined by selection against small-angle X-ray scattering data that incorporates the known structures of different fragments. We found that an ensemble of conformers reproduces small-angle X-ray scattering data better than a single structure suggesting in combination with molecular dynamics simulations that the hepatitis C virus (IRES) is an articulated molecule made of rigid parts that move relative to each other. Principal component analysis on an ensemble of physically accessible conformers of hepatitis C virus (IRES) revealed dominant collective motions in the molecule, which may underlie the conformational changes occurring in the (IRES) molecule upon formation of the initiation complex.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Structure of the full-length HCV IRES in solution

et al. 2013

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Functional Architecture of HCV IRES Domain II Stabilized by Divalent Metal Ions in the Crystal and in Solution

Dibrov¹,

Johnston-Cox²,

Weng³

et al. 2006

Angewandte Chemie

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The RNA genome of the hepatitis C virus (HCV) contains an internal ribosome entry site (IRES), which binds to the hostcell 40S ribosomal subunit and initiates protein translation in the absence of most initiation factors. [1,2] Recruitment of the ribosomal subunit to the HCV RNA is driven by the high affinity of the IRES-40S interaction.[3] The IRES sequence adopts a highly ordered secondary structure (Figure 1 a). [4] The three-dimensional architecture of the IRES is dominated by independently folding RNA domains.[5] Structures of IRES-40S complexes have been studied by cryo-electron microscopy (cryo-EM) revealing the overall shape of the RNA. [6,7] Higher-resolution structures of individual subdomains, including II [8] and IIIa-e, [9][10][11][12] have been determined by crystallography and NMR spectroscopy. Cryo-EM studies revealed that the domain II, which plays an important structural role in HCV translation, [13] adopts an L-shaped conformation that directs the apical hairpin loop IIb to overlap with the ribosomal E site in the proximity of the P site.[6] Binding of domain II induces a conformational change in the 40S head [7] and closes the messenger RNA (mRNA) binding cleft.[6] NMR studies suggested that subdomain IIa might be a flexible hinge whose bent state is stabilized by binding of divalent metal ions. [8] To investigate the molecular architecture of the IRES domain II kink and its metal-ion-dependent stabilization, we have used X-ray crystallography and structure-guided incorporation of fluorescent labels. For X-ray crystal structure determination (see Figure S4 and Table S1 in the Supporting Information), an oligonucleotide (IIa-1) was used that contained residues 49-69 and 100-115 of the HCV IRES (Figure 1). The overall structure of the RNA revealed a bent architecture for the IIa subdomain. The two stems that are flanking the internal bulge are arranged at a right angle (Figure 1 b). [14] The upper stem (residues 58-69/100-110) forms a continuous helix that contains both standard and noncanonical base pairs that adopt cis-Watson-Crick geometries. U106 is looped out from the stem to allow continuous stacking of the flanking base pairs. The arrangement of residues of the internal bulge introduces a right-angled bend in the RNA Figure 1. a) Secondary structure of the HCV 5'-nontranslated region that contains the IRES element and the subdomain IIa-1 construct used for crystallization and fluorescence labeling. The position of the IIa-1 construct within the IRES is indicated by a box. The nucleotides shown in red were changed in the construct from the HCV (genotype 1b) sequence to improve RNA stability. Non-Watson-Crick base pairs are indicated by "o" symbols. The numbering scheme for the construct has been adopted from the full HCV RNA. b) The three-dimensional structure of the IIa-1 RNA. 2007, 119, 230 -233 between the base pairs G52-C111 and C58-G110 that is stabilized by a combination of base stacking, hydrogen bonding, and metal-ion participation (see Figure 2 and Figure S5 in the Supporting ...

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