+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2603 | |||||||||
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Title | Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES | |||||||||
Map data | Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES in a partially rotated configuration | |||||||||
Sample |
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Keywords | translation.ribosome / eukaryote / initiaction | |||||||||
Biological species | Kluyveromyces lactis (yeast) / Cricket paralysis virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Fernandez IS / Bai X / Scheres SHW / Ramakrishnan V | |||||||||
Citation | Journal: Cell / Year: 2014 Title: Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome. Authors: Israel S Fernández / Xiao-Chen Bai / Garib Murshudov / Sjors H W Scheres / V Ramakrishnan / Abstract: The cricket paralysis virus internal ribosome entry site (CrPV-IRES) is a folded structure in a viral mRNA that allows initiation of translation in the absence of any host initiation factors. By ...The cricket paralysis virus internal ribosome entry site (CrPV-IRES) is a folded structure in a viral mRNA that allows initiation of translation in the absence of any host initiation factors. By using recent advances in single-particle electron cryomicroscopy, we have solved the structure of CrPV-IRES bound to the ribosome of the yeast Kluyveromyces lactis in both the canonical and rotated states at overall resolutions of 3.7 and 3.8 Å, respectively. In both states, the pseudoknot PKI of the CrPV-IRES mimics a tRNA/mRNA interaction in the decoding center of the A site of the 40S ribosomal subunit. The structure and accompanying factor-binding data show that CrPV-IRES binding mimics a pretranslocation rather than initiation state of the ribosome. Translocation of the IRES by elongation factor 2 (eEF2) is required to bring the first codon of the mRNA into the A site and to allow the start of translation. | |||||||||
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_2603.map.gz | 20.7 MB | EMDB map data format | |
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Header (meta data) | emd-2603-v30.xml emd-2603.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_2603.png | 351.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2603 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2603 | HTTPS FTP |
-Validation report
Summary document | emd_2603_validation.pdf.gz | 272.4 KB | Display | EMDB validaton report |
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Full document | emd_2603_full_validation.pdf.gz | 271.6 KB | Display | |
Data in XML | emd_2603_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2603 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2603 | HTTPS FTP |
-Related structure data
Related structure data | 4v92MC 2599C 2604C 4v91C M: atomic model generated by this map C: citing same article (ref.) |
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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_2603.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES in a partially rotated configuration | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 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 : Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES
Entire | Name: Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES |
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Components |
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-Supramolecule #1000: Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES
Supramolecule | Name: Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Experimental: 3.8 MDa / Theoretical: 3.8 MDa / Method: Sedimentation |
-Supramolecule #1: Kluyveromyces lactis 80S ribosome
Supramolecule | Name: Kluyveromyces lactis 80S ribosome / type: complex / ID: 1 / Name.synonym: Kluyveromyces lactis 80S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Kluyveromyces lactis (yeast) / Strain: Kluyveromyces lactis / synonym: Kluyveromyces lactis / Tissue: Kluyveromyces lactis / Cell: Kluyveromyces lactis / Organelle: Kluyveromyces lactis / Location in cell: Kluyveromyces lactis |
Molecular weight | Experimental: 3.2 MDa / Theoretical: 3.2 MDa |
-Macromolecule #1: CrPV-IRES
Macromolecule | Name: CrPV-IRES / type: protein_or_peptide / ID: 1 / Recombinant expression: No |
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Source (natural) | Organism: Cricket paralysis virus |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 6.5 Details: 10mM MES-KOH, 40mM K-acetate, 10mM NH4-acetated, 8mM Mg-acetate, 2mM DTT |
Grid | Details: 400mesh R2/2 Quantifoil grids |
Vitrification | Cryogen name: PROPANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Timed resolved state: 30 second incubation time / Method: 2.5 seconds blot |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Jul 7, 2013 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1900 / Average electron dose: 40 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.0018 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Sample movement corrected as implemented in Relion |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 28421 |
-Atomic model buiding 1
Initial model | PDB ID: 3u5b |
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Software | Name: Chimera, refmac |
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 60 / Target criteria: R-factor, FSC |
Output model | PDB-4v92: |
-Atomic model buiding 2
Initial model | PDB ID: 3u5d |
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Software | Name: Chimera, refmac |
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 60 / Target criteria: R-factor, FSC |
Output model | PDB-4v92: |
-Atomic model buiding 3
Initial model | PDB ID: 3u5c |
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Software | Name: Chimera, refmac |
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 60 / Target criteria: R-factor, FSC |
Output model | PDB-4v92: |