- EMDB-8123: Structure of the Kluyveromyces lactis 80S ribosome in complex wit... -
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Basic information
Entry
Database: EMDB / ID: EMD-8123
Title
Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2
Map data
None
Sample
eEF2 != Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2
eEF2
Complex: Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2
Other: x 2 types
RNA: x 3 types
Protein or peptide: x 78 types
Complex: Kluyveromyces lactis 80S ribosome
Complex: Cricket paralysis virus IRES
Complex: eEF2
Ligand: x 4 types
Keywords
ribosome / translocation / IRES / eEF2
Function / homology
Function and homology information
response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / protein-RNA complex assembly / translation regulator activity ...response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / protein-RNA complex assembly / translation regulator activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosome biogenesis / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function
60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 ...60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / : / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein L1, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein L1 signature. / : / Ribosomal protein S12e signature. / Ribosomal protein L1 / Ribosomal protein S12e / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / 40S Ribosomal protein S10 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / : / Ribosomal protein S7e signature. / Ribosomal protein L44e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / Ribosomal protein L13e / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L13e / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / : / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L44e / Ribosomal protein S30 / Ribosomal protein L44 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L30e signature 1. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal L40e family / Ribosomal protein S27e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein 60S L18 and 50S L18e / Ribosomal Protein L6, KOW domain / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L27e / Ribosomal protein S19e Similarity search - Domain/homology
60S ribosomal protein L8 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein eS32A / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Ubiquitin-ribosomal protein eS31 fusion protein ...60S ribosomal protein L8 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein eS32A / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Ubiquitin-ribosomal protein eS31 fusion protein / KLLA0F25542p / KLLA0F18040p / Ribosomal protein L15 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS5 / KLLA0F08261p / KLLA0F07843p / KLLA0F05247p / KLLA0F04675p / KLLA0F04499p / 40S ribosomal protein S12 / Small ribosomal subunit protein eS6 / KLLA0E23673p / KLLA0E23651p / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / KLLA0E12453p / KLLA0E12277p / 40S ribosomal protein S27 / KLLA0E06997p / KLLA0E06843p / KLLA0E05941p / Small ribosomal subunit protein uS14 / KLLA0E03455p / 60S ribosomal protein L29 / KLLA0D16027p / 60S ribosomal protein L36 / KLLA0D10659p / 40S ribosomal protein S3 / KLLA0D07405p / KLLA0D06941p / KLLA0D05643p / KLLA0D05181p / 40S ribosomal protein S26 / KLLA0D03410p / KLLA0C18216p / 40S ribosomal protein S7 / KLLA0C08371p / 40S ribosomal protein S24 / 40S ribosomal protein S30 / Ribosomal protein L37 / KLLA0B13409p / KLLA0B08173p / Small ribosomal subunit protein uS8 / KLLA0B07139p / 40S ribosomal protein S25 / 60S acidic ribosomal protein P0 / KLLA0B05742p / Small ribosomal subunit protein eS1 / KLLA0B04686p / 40S ribosomal protein S4 / KLLA0B02937p / Ribosomal protein / KLLA0B01562p / KLLA0B01474p / KLLA0A10483p / KLLA0A07227p / KLLA0A07194p / KLLA0A06336p / Small ribosomal subunit protein eS21 / 60S ribosomal protein L13 / RPS23 / Small ribosomal subunit protein uS9 / RPL28 / Ubiquitin fusion protein / : Similarity search - Component
Journal: Elife / Year: 2016 Title: Structural characterization of ribosome recruitment and translocation by type IV IRES. Authors: Jason Murray / Christos G Savva / Byung-Sik Shin / Thomas E Dever / V Ramakrishnan / Israel S Fernández / Abstract: Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps ...Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts tvhe otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation.
History
Deposition
Apr 13, 2016
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Header (metadata) release
May 18, 2016
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Map release
May 18, 2016
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Update
Apr 9, 2025
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Current status
Apr 9, 2025
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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