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Yorodumi- EMDB-11590: The Halastavi arva virus intergenic region IRES promotes translat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11590 | ||||||||||||||||||
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Title | The Halastavi arva virus intergenic region IRES promotes translation by the simplest possible initiation mechanism | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Function / homology | Function and homology information Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling ...Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Cyclin D associated events in G1 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Activation of NF-kappaB in B cells / L13a-mediated translational silencing of Ceruloplasmin expression / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SRP-dependent cotranslational protein targeting to membrane / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis Similarity search - Function | ||||||||||||||||||
Biological species | Halastavi arva RNA virus / Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||
Authors | Abaeva I / Vicens Q / Bochler A / Soufari H / Simonetti A / Pestova TV / Hashem Y / Hellen CUT | ||||||||||||||||||
Funding support | United States, France, 5 items
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Citation | Journal: Cell Rep / Year: 2020 Title: The Halastavi árva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism. Authors: Irina S Abaeva / Quentin Vicens / Anthony Bochler / Heddy Soufari / Angelita Simonetti / Tatyana V Pestova / Yaser Hashem / Christopher U T Hellen / Abstract: Dicistrovirus intergenic region internal ribosomal entry sites (IGR IRESs) do not require initiator tRNA, an AUG codon, or initiation factors and jumpstart translation from the middle of the ...Dicistrovirus intergenic region internal ribosomal entry sites (IGR IRESs) do not require initiator tRNA, an AUG codon, or initiation factors and jumpstart translation from the middle of the elongation cycle via formation of IRES/80S complexes resembling the pre-translocation state. eEF2 then translocates the [codon-anticodon]-mimicking pseudoknot I (PKI) from ribosomal A sites to P sites, bringing the first sense codon into the decoding center. Halastavi árva virus (HalV) contains an IGR that is related to previously described IGR IRESs but lacks domain 2, which enables these IRESs to bind to individual 40S ribosomal subunits. By using in vitro reconstitution and cryoelectron microscopy (cryo-EM), we now report that the HalV IGR IRES functions by the simplest initiation mechanism that involves binding to 80S ribosomes such that PKI is placed in the P site, so that the A site contains the first codon that is directly accessible for decoding without prior eEF2-mediated translocation of PKI. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11590.map.gz | 162.1 MB | EMDB map data format | |
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Header (meta data) | emd-11590-v30.xml emd-11590.xml | 102.7 KB 102.7 KB | Display Display | EMDB header |
Images | emd_11590.png | 203.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11590 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11590 | HTTPS FTP |
-Related structure data
Related structure data | 7a01MC 6zvkC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11590.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : COMPLEX BETWEEN 80S RIBOSOME AND HALV IGR IRES
+Supramolecule #1: COMPLEX BETWEEN 80S RIBOSOME AND HALV IGR IRES
+Supramolecule #2: Halastavi arva RNA virus
+Supramolecule #3: COMPLEX BETWEEN 80S RIBOSOME AND HALV IGR IRES
+Macromolecule #1: INTERNAL RIBOSOME ENTRY SITE
+Macromolecule #2: 28S RIBOSOMAL RNA
+Macromolecule #3: 5.8S RIBOSOMAL RNA
+Macromolecule #4: 5S RIBOSOMAL RNA
+Macromolecule #49: 18S RIBOSOMAL RNA
+Macromolecule #5: Uncharacterized protein
+Macromolecule #6: eL14
+Macromolecule #7: Ribosomal protein L24
+Macromolecule #8: Uncharacterized protein
+Macromolecule #9: Ribosomal protein L26
+Macromolecule #10: uL15
+Macromolecule #11: 60S ribosomal protein L29
+Macromolecule #12: uL4
+Macromolecule #13: eL31
+Macromolecule #14: eL32
+Macromolecule #15: 60S RIBOSOMAL PROTEIN UL13
+Macromolecule #16: eL33
+Macromolecule #17: eL34
+Macromolecule #18: Uncharacterized protein
+Macromolecule #19: uL29
+Macromolecule #20: 60S ribosomal protein L36
+Macromolecule #21: Ribosomal protein L37
+Macromolecule #22: ribosomal protein eL39
+Macromolecule #23: 60S RIBOSOMAL PROTEIN EL40
+Macromolecule #24: eL42
+Macromolecule #25: 60S ribosomal protein L5
+Macromolecule #26: uL22
+Macromolecule #27: ribosomal protein eL43
+Macromolecule #28: Uncharacterized protein
+Macromolecule #29: 60S acidic ribosomal protein P0
+Macromolecule #30: Ribosomal protein L10 (Predicted)
+Macromolecule #31: Uncharacterized protein
+Macromolecule #32: Ribosomal_L6e_N domain-containing protein
+Macromolecule #33: 60S RIBOSOMAL PROTEIN EL18
+Macromolecule #34: 60S ribosomal protein L6
+Macromolecule #35: uL30
+Macromolecule #36: 60S RIBOSOMAL PROTEIN EL8
+Macromolecule #37: Uncharacterized protein
+Macromolecule #38: Ribosomal protein L10 (Predicted)
+Macromolecule #39: Ribosomal protein L11
+Macromolecule #40: Ribosomal protein L14
+Macromolecule #41: Ribosomal protein L15
+Macromolecule #42: 60S ribosomal protein L27
+Macromolecule #43: 60S RIBOSOMAL PROTEIN EL19
+Macromolecule #44: Ribosomal protein
+Macromolecule #45: uL3
+Macromolecule #46: 60S RIBOSOMAL PROTEIN EL20
+Macromolecule #47: eL21
+Macromolecule #48: Ribosomal protein L22
+Macromolecule #50: 40S RIBOSOMAL PROTEIN ES30
+Macromolecule #51: Ribosomal protein L30
+Macromolecule #52: 40S ribosomal protein S27a
+Macromolecule #53: Ribosomal protein S11
+Macromolecule #54: ribosomal protein uS13
+Macromolecule #55: ribosomal protein RACK1
+Macromolecule #56: Uncharacterized protein
+Macromolecule #57: ribosomal protein uS19
+Macromolecule #58: Ribosomal protein S23
+Macromolecule #59: 40S_SA_C domain-containing protein
+Macromolecule #60: 40S ribosomal protein S3a
+Macromolecule #61: S5 DRBM domain-containing protein
+Macromolecule #62: 60s ribosomal protein l41
+Macromolecule #63: Ribosomal protein S3
+Macromolecule #64: 40S ribosomal protein S4,40S ribosomal protein S4
+Macromolecule #65: Ribosomal protein S15a
+Macromolecule #66: Ribosomal protein S5
+Macromolecule #67: 40S ribosomal protein S6
+Macromolecule #68: Uncharacterized protein
+Macromolecule #69: ribosomal protein eS28
+Macromolecule #70: ribosomal protein uS15
+Macromolecule #71: 40S ribosomal protein S8
+Macromolecule #72: Uncharacterized protein
+Macromolecule #73: Ribosomal protein S9 (Predicted)
+Macromolecule #74: 40S RIBOSOMAL PROTEIN ES21
+Macromolecule #75: 40S ribosomal protein S12
+Macromolecule #76: S10_plectin domain-containing protein
+Macromolecule #77: ribosomal protein uS14
+Macromolecule #78: Uncharacterized protein
+Macromolecule #79: 40S RIBOSOMAL PROTEIN ES7
+Macromolecule #80: Ribosomal_S10 domain-containing protein
+Macromolecule #81: 40S ribosomal protein S24
+Macromolecule #82: 40S ribosomal protein S27
+Macromolecule #83: ribosomal protein eS25
+Macromolecule #84: 40S RIBOSOMAL PROTEIN ES26
+Macromolecule #85: 60S ribosomal protein L13
+Macromolecule #86: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42135 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-7a01: |