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Open data
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Basic information
Entry | Database: PDB / ID: 4v91 | ||||||||||||
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Title | Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES | ||||||||||||
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![]() | RIBOSOME / TRANSLATION / INITIATION / IRES | ||||||||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
![]() | Fernandez, I.S. / Bai, X. / Scheres, S.H.W. / Ramakrishnan, V. | ||||||||||||
![]() | ![]() 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. | ||||||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 212.2 KB | Display | |
Data in CIF | ![]() | 364.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2599MC ![]() 2603C ![]() 2604C ![]() 4v92C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 3 types, 3 molecules 134
#1: RNA chain | Mass: 1097866.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+Protein , 41 types, 41 molecules ABCDEFGHIJLMNOPQRSTUVWXYZabcde...
-Protein/peptide , 1 types, 1 molecules n
#42: Protein/peptide | Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RIBOSOMAL PROTEIN EL41 / Source: (natural) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES Type: RIBOSOME |
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Buffer solution | pH: 6.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: PROPANE / Details: LIQUID ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jul 7, 2013 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 47000 X / Nominal defocus max: 3 nm / Nominal defocus min: 1.8 nm / Cs: 2.7 mm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 1900 |
Radiation wavelength | Relative weight: 1 |
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Processing
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CTF correction | Details: EACH PARTICLE | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: RELION / Resolution: 3.7 Å / Num. of particles: 18132 / Nominal pixel size: 1.34 Å / Symmetry type: POINT | ||||||||||||
Atomic model building | B value: 60 / Protocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: R-FACTOR, FSC / Details: METHOD--FLEXIBLE | ||||||||||||
Atomic model building | PDB-ID: 3B31 | ||||||||||||
Refinement | Highest resolution: 3.7 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.7 Å
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