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5it7

From Proteopedia

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Current revision

Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2

5it7, resolution 3.60Å

Structural highlights

5it7 is a 10 chain structure with sequence from Kluyveromyces lactis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.6Å
Ligands:
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q6CQM3_KLULA

Publication Abstract from PubMed

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 (Fernandez 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.

Structural characterization of ribosome recruitment and translocation by type IV IRES.,Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernandez IS Elife. 2016 May 9;5. pii: e13567. doi: 10.7554/eLife.13567. PMID:27159451^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Murray J, Savva CG, Shin BS, Dever TE, Ramakrishnan V, Fernandez IS. Structural characterization of ribosome recruitment and translocation by type IV IRES. Elife. 2016 May 9;5. pii: e13567. doi: 10.7554/eLife.13567. PMID:27159451 doi:http://dx.doi.org/10.7554/eLife.13567

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5it7"

@@ Line 3: / Line 3: @@
 <SX load='5it7' size='340' side='right' viewer='molstar' caption='[[5it7]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5it7]] is a 83 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Atcc_56498 Atcc 56498], [http://en.wikipedia.org/wiki/Kluyveromyces_lactis Kluyveromyces lactis] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_p283 Saccharomyces cerevisiae p283]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IT7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IT7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5it7]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_lactis Kluyveromyces lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IT7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IT7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6EM:(2S)-1-AMINO-N,N,N-TRIMETHYL-1-OXOBUTAN-2-AMINIUM'>6EM</scene>, <scene name='pdbligand=GCP:PHOSPHOMETHYLPHOSPHONIC+ACID+GUANYLATE+ESTER'>GCP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.6&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6EM:(2S)-1-AMINO-N,N,N-TRIMETHYL-1-OXOBUTAN-2-AMINIUM'>6EM</scene>, <scene name='pdbligand=GCP:PHOSPHOMETHYLPHOSPHONIC+ACID+GUANYLATE+ESTER'>GCP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Eft2, P283_D20866 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1177187 Saccharomyces cerevisiae P283])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5it7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5it7 OCA], [https://pdbe.org/5it7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5it7 RCSB], [https://www.ebi.ac.uk/pdbsum/5it7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5it7 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5it7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5it7 OCA], [http://pdbe.org/5it7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5it7 RCSB], [http://www.ebi.ac.uk/pdbsum/5it7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5it7 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RSSA_KLULA RSSA_KLULA]] Required for the assembly and/or stability of the 40S ribosomal subunit. Required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits. [[http://www.uniprot.org/uniprot/RS21_KLULA RS21_KLULA]] Required for the processing of the 20S rRNA-precursor to mature 18S rRNA in a late step of the maturation of 40S ribosomal subunits. Has a physiological role leading to 18S rRNA stability (By similarity). [[http://www.uniprot.org/uniprot/RS27A_KLULA RS27A_KLULA]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, and DNA-damage responses. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).  Ribosomal protein S27a is a component of the 40S subunit of the ribosome. [[http://www.uniprot.org/uniprot/Q6CW89_KLULA Q6CW89_KLULA]] Ribosomal protein P0 is the functional equivalent of E.coli protein L10.[PIRNR:PIRNR039087] [[http://www.uniprot.org/uniprot/Q6CUW0_KLULA Q6CUW0_KLULA]] Binds to the 23S rRNA.[RuleBase:RU000576]
+[https://www.uniprot.org/uniprot/Q6CQM3_KLULA Q6CQM3_KLULA]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </SX>
-[[Category: Atcc 56498]]
 [[Category: Kluyveromyces lactis]]
 [[Category: Large Structures]]
-[[Category: Saccharomyces cerevisiae p283]]
+[[Category: Dever TE]]
-[[Category: Dever, T E]]
+[[Category: Fernandez IS]]
-[[Category: Fernandez, I S]]
+[[Category: Murray J]]
-[[Category: Murray, J]]
+[[Category: Ramakrishnan V]]
-[[Category: Ramakrishnan, V]]
+[[Category: Savva CG]]
-[[Category: Savva, C G]]
+[[Category: Shin BS]]
-[[Category: Shin, B S]]
-[[Category: Eef2]]
-[[Category: Ire]]
-[[Category: Ribosome]]
-[[Category: Translocation]]

5it7

From Proteopedia

Current revision

Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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