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Yorodumi- EMDB-35041: Cryo-EM structure of the J-K-St region of EMCV IRES in complex wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35041 | |||||||||
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Title | Cryo-EM structure of the J-K-St region of EMCV IRES in complex with eIF4G-HEAT1 and eIF4A | |||||||||
Map data | Post-process map | |||||||||
Sample |
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Keywords | Translation initiation factors / Translation / RNA binding protein | |||||||||
Function / homology | Function and homology information positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / positive regulation of translation in response to endoplasmic reticulum stress / macromolecule biosynthetic process / regulation of cellular response to stress / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / cap-dependent translational initiation / eukaryotic initiation factor 4E binding / nuclear stress granule / RNA cap binding ...positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / positive regulation of translation in response to endoplasmic reticulum stress / macromolecule biosynthetic process / regulation of cellular response to stress / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / cap-dependent translational initiation / eukaryotic initiation factor 4E binding / nuclear stress granule / RNA cap binding / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / Deadenylation of mRNA / miRNA-mediated gene silencing by inhibition of translation / M-decay: degradation of maternal mRNAs by maternally stored factors / positive regulation of protein localization to cell periphery / regulation of translational initiation / Ribosomal scanning and start codon recognition / Translation initiation complex formation / negative regulation of peptidyl-threonine phosphorylation / mTORC1-mediated signalling / regulation of presynapse assembly / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / behavioral fear response / cellular response to nutrient levels / positive regulation of G1/S transition of mitotic cell cycle / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / energy homeostasis / translation initiation factor binding / positive regulation of protein metabolic process / positive regulation of neuron differentiation / translation initiation factor activity / negative regulation of autophagy / helicase activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / translational initiation / lung development / neuron differentiation / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / cytoplasmic stress granule / double-stranded RNA binding / positive regulation of peptidyl-serine phosphorylation / positive regulation of cell growth / response to ethanol / postsynapse / molecular adaptor activity / RNA helicase activity / ribosome / RNA helicase / translation / mRNA binding / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Encephalomyocarditis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.76 Å | |||||||||
Authors | Suzuki H / Fujiyoshi Y / Imai S / Shimada I | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Dynamically regulated two-site interaction of viral RNA to capture host translation initiation factor. Authors: Shunsuke Imai / Hiroshi Suzuki / Yoshinori Fujiyoshi / Ichio Shimada / Abstract: Many RNA viruses employ internal ribosome entry sites (IRESs) in their genomic RNA to commandeer the host's translational machinery for replication. The IRES from encephalomyocarditis virus (EMCV) ...Many RNA viruses employ internal ribosome entry sites (IRESs) in their genomic RNA to commandeer the host's translational machinery for replication. The IRES from encephalomyocarditis virus (EMCV) interacts with eukaryotic translation initiation factor 4 G (eIF4G), recruiting the ribosomal subunit for translation. Here, we analyze the three-dimensional structure of the complex composed of EMCV IRES, the HEAT1 domain fragment of eIF4G, and eIF4A, by cryo-electron microscopy. Two distinct eIF4G-interacting domains on the IRES are identified, and complex formation changes the angle therebetween. Further, we explore the dynamics of these domains by using solution NMR spectroscopy, revealing conformational equilibria in the microsecond to millisecond timescale. In the lowly-populated conformations, the base-pairing register of one domain is shifted with the structural transition of the three-way junction, as in the complex structure. Our study provides insights into the viral RNA's sophisticated strategy for optimal docking to hijack the host protein. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35041.map.gz | 8.5 MB | EMDB map data format | |
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Header (meta data) | emd-35041-v30.xml emd-35041.xml | 21.4 KB 21.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35041_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_35041.png | 121.9 KB | ||
Masks | emd_35041_msk_1.map | 9.2 MB | Mask map | |
Others | emd_35041_half_map_1.map.gz emd_35041_half_map_2.map.gz | 8.5 MB 8.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35041 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35041 | HTTPS FTP |
-Validation report
Summary document | emd_35041_validation.pdf.gz | 909.8 KB | Display | EMDB validaton report |
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Full document | emd_35041_full_validation.pdf.gz | 909.4 KB | Display | |
Data in XML | emd_35041_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_35041_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35041 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35041 | HTTPS FTP |
-Related structure data
Related structure data | 8hujMC 8j7rC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35041.map.gz / Format: CCP4 / Size: 9.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Post-process map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1475 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_35041_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35041_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35041_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of the J-K-St region of EMCV IRES with eIF4A and ...
Entire | Name: Ternary complex of the J-K-St region of EMCV IRES with eIF4A and eIF4G-HEAT1 |
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Components |
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-Supramolecule #1: Ternary complex of the J-K-St region of EMCV IRES with eIF4A and ...
Supramolecule | Name: Ternary complex of the J-K-St region of EMCV IRES with eIF4A and eIF4G-HEAT1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Eukaryotic initiation factor 4A-I
Macromolecule | Name: Eukaryotic initiation factor 4A-I / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 48.659434 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH HHSSGLEVLF QGPSASQDSR SRDNGPDGME PEGVIESNWN EIVDSFDDMN LSESLLRGIY AYGFEKPSAI QQRAILPCI KGYDVIAQAQ SGTGKTATFA ISILQQIELD LKATQALVLA PTRELAQQIQ KVVMALGDYM GASCHACIGG T NVRAEVQK ...String: MGSSHHHHHH HHSSGLEVLF QGPSASQDSR SRDNGPDGME PEGVIESNWN EIVDSFDDMN LSESLLRGIY AYGFEKPSAI QQRAILPCI KGYDVIAQAQ SGTGKTATFA ISILQQIELD LKATQALVLA PTRELAQQIQ KVVMALGDYM GASCHACIGG T NVRAEVQK LQMEAPHIIV GTPGRVFDML NRRYLSPKYI KMFVLDEADE MLSRGFKDQI YDIFQKLNSN TQVVLLSATM PS DVLEVTK KFMRDPIRIL VKKEELTLEG IRQFYINVER EEWKLDTLCD LYETLTITQA VIFINTRRKV DWLTEKMHAR DFT VSAMHG DMDQKERDVI MREFRSGSSR VLITTDLLAR GIDVQQVSLV INYDLPTNRE NYIHRIGRGG RFGRKGVAIN MVTE EDKRT LRDIETFYNT SIEEMPLNVA DLI UniProtKB: Eukaryotic initiation factor 4A-I |
-Macromolecule #2: Eukaryotic translation initiation factor 4 gamma 1
Macromolecule | Name: Eukaryotic translation initiation factor 4 gamma 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 31.786811 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MNHKVHHHHH HIEGRHMELG TLEDRGEEDA DGSKTQDLFR RVRSILNKLT PQMFQQLMKQ VTQLAIDTEE RLKGVIDLIF EKAISEPNF SVAYANMCRC LMALKVPTTE KPTVTVNFRK LLLNRCQKEF EKDKDDDEVF EKKQKEMDEA ATAEERGRLK E ELEEARDI ...String: MNHKVHHHHH HIEGRHMELG TLEDRGEEDA DGSKTQDLFR RVRSILNKLT PQMFQQLMKQ VTQLAIDTEE RLKGVIDLIF EKAISEPNF SVAYANMCRC LMALKVPTTE KPTVTVNFRK LLLNRCQKEF EKDKDDDEVF EKKQKEMDEA ATAEERGRLK E ELEEARDI ARRRSLGNIK FIGELFKLKM LTEAIMHDCV VKLLKNHDEE SLECLCRLLT TIGKDLDFEK AKPRMDQYFN QM EKIIKEK KTSSRIRFML QDVLDLRGSN WVP UniProtKB: Eukaryotic translation initiation factor 4 gamma 1 |
-Macromolecule #3: IRES RNA (J-K-St)
Macromolecule | Name: IRES RNA (J-K-St) / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Encephalomyocarditis virus |
Molecular weight | Theoretical: 34.838609 KDa |
Sequence | String: GGGGCUGAAG GAUGCCCAGA AGGUACCCCA UUGUAUGGGA UCUGAUCUGG GGCCUCGGUG CACAUGCUUU ACAUGUGUUU AGUCGAGGU UAAAAAACGU CUAGGCCCC GENBANK: GENBANK: NC_001479.1 |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 1 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Details | The microscope model is the JEOL's "JEM-Z320FHC", the custom-built model equipped with a helium-cooled specimen stage. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 2 / Number real images: 6194 / Average exposure time: 8.0 sec. / Average electron dose: 71.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.4 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-8huj: |