6yal: Difference between revisions

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<StructureSection load='6yal' size='340' side='right'caption='[[6yal]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
<StructureSection load='6yal' size='340' side='right'caption='[[6yal]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6yal]] is a 41 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YAL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YAL FirstGlance]. <br>
<table><tr><td colspan='2'>[[6yal]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YAL FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C4J:'>C4J</scene>, <scene name='pdbligand=T6A:N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL)CARBAMOYL]THREONINE-5-MONOPHOSPHATE'>T6A</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C4J:(5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-L-arabinitol'>C4J</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=T6A:N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL)CARBAMOYL]THREONINE-5-MONOPHOSPHATE'>T6A</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6yam|6yam]], [[6yan|6yan]]</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=6yal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yal OCA], [https://pdbe.org/6yal PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yal RCSB], [https://www.ebi.ac.uk/pdbsum/6yal PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yal 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=6yal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yal OCA], [http://pdbe.org/6yal PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yal RCSB], [http://www.ebi.ac.uk/pdbsum/6yal PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yal ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/G1TLT8_RABIT G1TLT8_RABIT]] 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. Also functions as a cell surface receptor for laminin. Plays a role in cell adhesion to the basement membrane and in the consequent activation of signaling transduction pathways. May play a role in cell fate determination and tissue morphogenesis. Also acts as a receptor for several other ligands, including the pathogenic prion protein, viruses, and bacteria. Acts as a PPP1R16B-dependent substrate of PPP1CA.[HAMAP-Rule:MF_03016] [[http://www.uniprot.org/uniprot/G1TN72_RABIT G1TN72_RABIT]] May play a role during erythropoiesis through regulation of transcription factor DDIT3 (By similarity).[HAMAP-Rule:MF_03122]  
[https://www.uniprot.org/uniprot/RS32_RABIT RS32_RABIT] Component of the small ribosomal subunit (PubMed:24995983, PubMed:27863242). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:24995983, PubMed:27863242). Interacts with the beta subunit of protein kinase CKII and stimulates phosphorylation of DNA topoisomerase II alpha by CKII (By similarity).[UniProtKB:P62945]<ref>PMID:24995983</ref> <ref>PMID:27863242</ref>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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</div>
</div>
<div class="pdbe-citations 6yal" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 6yal" style="background-color:#fffaf0;"></div>
==See Also==
*[[Eukaryotic initiation factor 3D structures|Eukaryotic initiation factor 3D structures]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
*[[3D sructureseceptor for activated protein kinase C 1|3D sructureseceptor for activated protein kinase C 1]]
== References ==
== References ==
<references/>
<references/>
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[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Oryctolagus cuniculus]]
[[Category: Oryctolagus cuniculus]]
[[Category: Bochler, A]]
[[Category: Bochler A]]
[[Category: Guca, E]]
[[Category: Guca E]]
[[Category: Hashem, Y]]
[[Category: Hashem Y]]
[[Category: Simonetti, A]]
[[Category: Simonetti A]]
[[Category: Abce1]]
[[Category: Eif1a]]
[[Category: Eif3]]
[[Category: Initiation complex]]
[[Category: Rabbit]]
[[Category: Translation]]

Latest revision as of 13:44, 23 October 2024

Mammalian 48S late-stage initiation complex with beta-globin mRNAMammalian 48S late-stage initiation complex with beta-globin mRNA

Structural highlights

6yal is a 10 chain structure with sequence from Oryctolagus cuniculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Electron Microscopy, Resolution 3Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS32_RABIT Component of the small ribosomal subunit (PubMed:24995983, PubMed:27863242). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:24995983, PubMed:27863242). Interacts with the beta subunit of protein kinase CKII and stimulates phosphorylation of DNA topoisomerase II alpha by CKII (By similarity).[UniProtKB:P62945][1] [2]

Publication Abstract from PubMed

In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, beta-globin and histone 4, at overall resolution of 3 and 3.5 A, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC.

Structural Insights into the Mammalian Late-Stage Initiation Complexes.,Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y Cell Rep. 2020 Apr 7;31(1):107497. doi: 10.1016/j.celrep.2020.03.061. PMID:32268096[3]

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

See Also

References

  1. ↑ Budkevich TV, Giesebrecht J, Behrmann E, Loerke J, Ramrath DJ, Mielke T, Ismer J, Hildebrand PW, Tung CS, Nierhaus KH, Sanbonmatsu KY, Spahn CM. Regulation of the Mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement. Cell. 2014 Jul 3;158(1):121-31. doi: 10.1016/j.cell.2014.04.044. PMID:24995983 doi:http://dx.doi.org/10.1016/j.cell.2014.04.044
  2. ↑ Shao S, Murray J, Brown A, Taunton J, Ramakrishnan V, Hegde RS. Decoding Mammalian Ribosome-mRNA States by Translational GTPase Complexes. Cell. 2016 Nov 17;167(5):1229-1240.e15. doi: 10.1016/j.cell.2016.10.046. PMID:27863242 doi:http://dx.doi.org/10.1016/j.cell.2016.10.046
  3. ↑ Simonetti A, Guca E, Bochler A, Kuhn L, Hashem Y. Structural Insights into the Mammalian Late-Stage Initiation Complexes. Cell Rep. 2020 Apr 7;31(1):107497. doi: 10.1016/j.celrep.2020.03.061. PMID:32268096 doi:http://dx.doi.org/10.1016/j.celrep.2020.03.061

6yal, resolution 3.00Å

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