Rabbit ribosomal 80S elongation complex with eEF1A, A*/T Ala-tRNA, P site Ala-tRNA, E site Ala-tRNA on NediV ORF
マップデータ
試料
複合体: NediV IRES (P-site) in complex with Rabbit 80S
タンパク質・ペプチド: x 63種
RNA: x 3種
RNA: x 4種
タンパク質・ペプチド: x 15種
リガンド: x 3種
キーワード
Ribosome / IRES / Translation / Initiation
機能・相同性
機能・相同性情報
guanyl nucleotide binding / kinase activator activity / translational elongation / ubiquitin ligase inhibitor activity / translation elongation factor activity / 90S preribosome / positive regulation of signal transduction by p53 class mediator / phagocytic cup / protein-RNA complex assembly / gastrulation ...guanyl nucleotide binding / kinase activator activity / translational elongation / ubiquitin ligase inhibitor activity / translation elongation factor activity / 90S preribosome / positive regulation of signal transduction by p53 class mediator / phagocytic cup / protein-RNA complex assembly / gastrulation / translation regulator activity / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / MDM2/MDM4 family protein binding / cellular response to epidermal growth factor stimulus / positive regulation of apoptotic signaling pathway / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / spindle / cytoplasmic ribonucleoprotein granule / rRNA processing / regulation of translation / rhythmic process / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / killing of cells of another organism / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / perikaryon / cell differentiation / cytoplasmic translation / tRNA binding / mitochondrial inner membrane / postsynaptic density / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / mRNA binding / GTPase activity / centrosome / apoptotic process / nucleolus / synapse / dendrite / GTP binding / perinuclear region of cytoplasm / endoplasmic reticulum / DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能
Translation elongation factor EF1A, eukaryotic/archaeal / : / GTP-eEF1A C-terminal domain-like / : / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus ...Translation elongation factor EF1A, eukaryotic/archaeal / : / GTP-eEF1A C-terminal domain-like / : / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / 50S ribosomal protein L10, insertion domain superfamily / Ubiquitin-like protein FUBI / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L30e / Tr-type G domain, conserved site / Ribosomal protein L28e / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal L15/L27a, N-terminal / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Translation elongation factor EFTu-like, domain 2 / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L13e / Elongation factor Tu domain 2 / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Ribosomal protein L10e, conserved site / 40S Ribosomal protein S10 / Ribosomal protein L10e signature. / S27a-like superfamily / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Ribosomal protein L19/L19e conserved site / Plectin/S10 domain / Ribosomal protein L19e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L23, N-terminal domain / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal L40e family / Ribosomal protein L36e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L30e signature 1. / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / : / Ribosomal protein L35Ae, conserved site / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein L35Ae signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L44e / : / Ribosomal protein L44 / Ribosomal protein S7e signature. / Ribosomal protein 60S L18 and 50S L18e / 60S ribosomal protein L35 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a 類似検索 - ドメイン・相同性
Small ribosomal subunit protein eS32 / Ribosomal protein L36a / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 ...Small ribosomal subunit protein eS32 / Ribosomal protein L36a / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein eS7 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein uS11 / 40S ribosomal protein S24 / Large ribosomal subunit protein uL14 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / 40S ribosomal protein S4 / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL18 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL27 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL38 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL28 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS5 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein uL18 / Elongation factor 1-alpha 1 / Large ribosomal subunit protein eL37 類似検索 - 構成要素
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R35 GM139453
米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R35 GM122602
米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
R01 GM097014
米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
R21 AI188505
米国
引用
ジャーナル: Nucleic Acids Res / 年: 2026 タイトル: Structural studies of nedicistrovirus IRES-driven, initiation factor-independent translation shed light on key steps of eukaryotic translation elongation. 著者: Swastik De / Clara G Altomare / Irina S Abaeva / Prikshat Dadhwal / Priyanka Garg / Francisco Acosta-Reyes / Zuben P Brown / Tatyana V Pestova / Christopher U T Hellen / Joachim Frank / 要旨: We utilized the nedicistrovirus (NediV) intergenic region (IGR) internal ribosomal entry site (IRES)-mediated, initiation factor-independent translation initiation system and determined high- ...We utilized the nedicistrovirus (NediV) intergenic region (IGR) internal ribosomal entry site (IRES)-mediated, initiation factor-independent translation initiation system and determined high-resolution structures of 80S ribosome complexes with the NediV IRES in various functional states, including binary complexes, aminoacyl-transfer RNA (tRNA)-bound complexes, and complexes with elongation factor eEF2. In binary complexes, the NediV IRES primarily occupies the ribosomal P site, exhibiting conformational flexibility and engaging the ribosome at multiple interaction sites. Upon translocation, the IRES undergoes structural rearrangements, including destabilization of its PKI domain, facilitating the transition to canonical elongation. Crucially, we captured an eEF2-bound complex, along with an eEF1A-bound failed decoding complex featuring a mismatched tRNA, the latter representing the first instance of a canonical elongation complex visualized in the presence of a natural, hydrolysable nucleotide and without the addition of any trapping agents. These findings provide a comprehensive structural overview of IGR IRES-mediated translation initiation and its transition to elongation, revealing key mechanistic details of viral translation and proofreading.