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- PDB-5it7: Structure of the Kluyveromyces lactis 80S ribosome in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5it7 | ||||||||||||
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Title | Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2 | ||||||||||||
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![]() | RIBOSOME / translocation / IRES / eEF2 | ||||||||||||
Function / homology | ![]() response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity ...response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
![]() | Murray, J. / Savva, C.G. / Shin, B.S. / Dever, T.E. / Ramakrishnan, V. / Fernandez, I.S. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural characterization of ribosome recruitment and translocation by type IV IRES. Authors: Jason Murray / Christos G Savva / Byung-Sik Shin / Thomas E Dever / V Ramakrishnan / Israel S Fernández / ![]() ![]() Abstract: Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps ...Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts tvhe otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation. | ||||||||||||
History |
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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 | ![]() | 5.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 366.6 KB | Display | |
Data in CIF | ![]() | 630.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8123MC ![]() 8124C ![]() 5it9C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA/RNA hybrid , 2 types, 2 molecules 54
#1: DNA/RNA hybrid | Mass: 1056706.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#82: DNA/RNA hybrid | Mass: 60732.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-RNA chain , 3 types, 3 molecules 782
#2: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#3: RNA chain | Mass: 50293.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#81: RNA chain | Mass: 579239.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+Protein , 52 types, 52 molecules AACCDDEEFFGGHHIIJJMMOOPPQQRRTTUUVVYYZZaabbddeeffgghhkkmmppqq...
-60S ribosomal protein ... , 10 types, 10 molecules BBLLSSWWXXcciillnnoo
#5: Protein | Mass: 43422.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#14: Protein | Mass: 22441.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#21: Protein | Mass: 20046.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#25: Protein | Mass: 7279.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#26: Protein | Mass: 13700.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#31: Protein | Mass: 10511.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#37: Protein | Mass: 10925.905 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#40: Protein/peptide | Mass: 6114.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P04650 |
#42: Protein/peptide | Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P0CX86 |
#43: Protein | Mass: 11676.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Ribosomal protein ... , 2 types, 2 molecules NNjj
#16: Protein | Mass: 24193.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#38: Protein | Mass: 9679.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-40S ribosomal protein ... , 14 types, 14 molecules ABEGIMOQVWYbcd
#48: Protein | Mass: 22882.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#49: Protein | Mass: 24488.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#52: Protein | Mass: 29486.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#54: Protein | Mass: 25810.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#56: Protein | Mass: 22511.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#60: Protein | Mass: 13124.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#62: Protein | Mass: 13458.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#64: Protein | Mass: 15656.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#69: Protein | Mass: 9797.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#70: Protein | Mass: 14513.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#72: Protein | Mass: 15063.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#75: Protein | Mass: 8884.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#76: Protein | Mass: 7073.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#77: Protein | Mass: 6322.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 4 types, 88 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GCP.gif)
![](data/chem/img/6EM.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GCP.gif)
![](data/chem/img/6EM.gif)
#84: Chemical | ChemComp-MG / #85: Chemical | ChemComp-ZN / #86: Chemical | ChemComp-GCP / | #87: Chemical | ChemComp-6EM / ( | |
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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 |
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Molecular weight | Value: 4 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 6.5 | ||||||||||||||||||||||||||||||
Buffer component | Conc.: 20 mM / Name: MES-KOH | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: 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 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37844 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: RECIPROCAL |