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- EMDB-11459: The Halastavi arva virus (HalV) intergenic region IRES promotes t... -
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Basic information
Entry | Database: EMDB / ID: EMD-11459 | ||||||||||||||||||
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Title | The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the simplest possible initiation mechanism | ||||||||||||||||||
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![]() | RIBOSOME INTERNAL RIBOSOME ENTRY SITE RNA DICISTROVIRUS Halastavi arva virus Intergenic region pseudoknot CrPV IGR IRES SERBP1 / TRANSLATION | ||||||||||||||||||
Function / homology | ![]() Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin ...Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / APC/C:Cdc20 mediated degradation of Cyclin B / 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 / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of PLK1 Activity at G2/M Transition / Regulation of innate immune responses to cytosolic DNA / Autodegradation of the E3 ubiquitin ligase COP1 / RAD18 and ubiquitinated PCNA-mediated recruitment of translesion polymerases / Nucleotide Excision Repair / Deactivation of the beta-catenin transactivating complex / TRAF6 mediated induction of proinflammatory cytokines / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / NFkB activation mediated by RIP1 complexed with activated TLR3 / Activated TAK1 mediates p38 MAP kinase phosphorylation / Activated TAK1 mediates Jun kinases (JNK) phosphorylation and activation / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of AXIN / Degradation of DVL / Regulation of FZD by ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Hedgehog 'on' state / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / TNFR2 non-canonical NF-kB pathway / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Ovarian tumor domain proteases / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / NFkB and MAPK activation mediated by TRAF6 upon TLR7 or TLR21 stimulation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / : / CDK-mediated phosphorylation and removal of Cdc6 / Stabilization of p53 / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Downregulation of ERBB2 signaling / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of PTEN localization / Regulation of PTEN stability and activity / ER Quality Control Compartment (ERQC) / Peroxisomal protein import / 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 / Pexophagy / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Downregulation of TGF-beta receptor signaling / Antigen processing: Ubiquitination & Proteasome degradation / DNA Damage Recognition in GG-NER / Orc1 removal from chromatin / Regulation of signaling by CBL / TRAF mediated activation of IRF Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.49 Å | ||||||||||||||||||
![]() | Abaeva IS / Vicens Q | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 164.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 109.7 KB 109.7 KB | Display Display | ![]() |
Images | ![]() | 126.4 KB | ||
Filedesc metadata | ![]() | 19.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zvkMC ![]() 7a01C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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Sample components
+Entire : COMPLEX BETWEEN 870S RIBOSOME AND HALV IGR IRES
+Supramolecule #1: COMPLEX BETWEEN 870S RIBOSOME AND HALV IGR IRES
+Supramolecule #2: RIBOSOME
+Supramolecule #3: HALV IGR IRES
+Macromolecule #1: Ribosomal protein L14
+Macromolecule #5: 60S RIBOSOMAL PROTEIN EL38
+Macromolecule #6: 60S RIBOSOMAL PROTEIN UL13
+Macromolecule #7: uL22
+Macromolecule #8: 60S RIBOSOMAL PROTEIN EL18
+Macromolecule #9: 60S RIBOSOMAL PROTEIN EL19
+Macromolecule #10: uL3
+Macromolecule #11: 60S RIBOSOMAL PROTEIN EL20
+Macromolecule #12: eL21
+Macromolecule #13: Ribosomal protein L22
+Macromolecule #14: eL14
+Macromolecule #15: Ribosomal protein L24
+Macromolecule #16: 60S RIBOSOMAL PROTEIN UL23
+Macromolecule #17: Ribosomal protein L26
+Macromolecule #18: uL15
+Macromolecule #19: 60S ribosomal protein L29
+Macromolecule #20: Ribosomal protein L30
+Macromolecule #21: uL4
+Macromolecule #22: eL31
+Macromolecule #23: eL32
+Macromolecule #24: eL33
+Macromolecule #25: eL34
+Macromolecule #26: 60S RIBOSOMAL PROTEIN UL2
+Macromolecule #27: uL29
+Macromolecule #28: 60S ribosomal protein L36
+Macromolecule #29: Ribosomal protein L37
+Macromolecule #30: ribosomal protein eL39
+Macromolecule #31: 60S RIBOSOMAL PROTEIN EL40
+Macromolecule #32: eL42
+Macromolecule #33: 60S ribosomal protein L5
+Macromolecule #34: ribosomal protein eL43
+Macromolecule #35: 60S RIBOSOMAL PROTEIN EL28
+Macromolecule #36: 60S acidic ribosomal protein P0
+Macromolecule #37: Ribosomal protein L10 (Predicted)
+Macromolecule #38: Uncharacterized protein
+Macromolecule #39: Ribosomal_L6e_N domain-containing protein
+Macromolecule #40: 60S ribosomal protein L6
+Macromolecule #41: uL30
+Macromolecule #42: 60S RIBOSOMAL PROTEIN EL8
+Macromolecule #43: 60S RIBOSOMAL PROTEIN UL6
+Macromolecule #44: Ribosomal protein L10 (Predicted)
+Macromolecule #45: Ribosomal protein L11
+Macromolecule #46: 60S ribosomal protein L13
+Macromolecule #47: Ribosomal protein L15
+Macromolecule #48: 60S ribosomal protein L27
+Macromolecule #49: Ribosomal protein
+Macromolecule #51: Ribosomal_S10 domain-containing protein
+Macromolecule #52: 40S RIBOSOMAL PROTEIN ES30
+Macromolecule #53: Ribosomal protein S11
+Macromolecule #54: ribosomal protein eS28
+Macromolecule #56: 40S RIBOSOMAL PROTEIN ES7
+Macromolecule #57: 40S RIBOSOMAL PROTEIN US11
+Macromolecule #58: ribosomal protein uS19
+Macromolecule #59: 40S RIBOSOMAL PROTEIN US9
+Macromolecule #60: 40S RIBOSOMAL PROTEIN ES17
+Macromolecule #61: 40S RIBOSOMAL PROTEIN ES21
+Macromolecule #62: ribosomal protein uS13
+Macromolecule #63: 40S RIBOSOMAL PROTEIN ES19
+Macromolecule #64: Ribosomal protein S15a
+Macromolecule #65: 40S ribosomal protein S24
+Macromolecule #66: 40S ribosomal protein S27
+Macromolecule #67: ribosomal protein eS25
+Macromolecule #68: 40S RIBOSOMAL PROTEIN ES26
+Macromolecule #69: 40S RIBOSOMAL PROTEIN ES31
+Macromolecule #70: ribosomal protein RACK1
+Macromolecule #71: Ribosomal protein S23
+Macromolecule #72: 40S_SA_C domain-containing protein
+Macromolecule #73: 40S ribosomal protein S3a
+Macromolecule #74: S5 DRBM domain-containing protein
+Macromolecule #75: 60s ribosomal protein l41
+Macromolecule #76: Ribosomal protein S3
+Macromolecule #77: 40S ribosomal protein S4
+Macromolecule #78: Ribosomal protein S5
+Macromolecule #79: 40S ribosomal protein S6
+Macromolecule #80: 40S ribosomal protein S8
+Macromolecule #81: Ribosomal protein S9 (Predicted)
+Macromolecule #82: 40S ribosomal protein S12
+Macromolecule #83: ribosomal protein uS15
+Macromolecule #84: S10_plectin domain-containing protein
+Macromolecule #85: ribosomal protein uS14
+Macromolecule #2: 28S RIBOSOMAL RNA
+Macromolecule #3: 5S RIBOSOMAL RNA
+Macromolecule #4: 5.8S RIBOSOMAL RNA
+Macromolecule #50: INTERNAL RIBOSOME ENTRY SITE
+Macromolecule #55: 18S RIBOSOMAL RNA
+Macromolecule #86: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55589 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |