4v8p: Difference between revisions

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<StructureSection load='4v8p' size='340' side='right'caption='[[4v8p]], [[Resolution|resolution]] 3.52&Aring;' scene=''>
<StructureSection load='4v8p' size='340' side='right'caption='[[4v8p]], [[Resolution|resolution]] 3.52&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4v8p]] is a 184 chain structure with sequence from [http://en.wikipedia.org/wiki/Tetrahymena_thermophila Tetrahymena thermophila]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a17 4a17], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a18 4a18], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a19 4a19], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a1a 4a1a], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a1b 4a1b], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a1c 4a1c], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a1d 4a1d] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a1e 4a1e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V8P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V8P FirstGlance]. <br>
<table><tr><td colspan='2'>[[4v8p]] is a 40 chain structure with sequence from [https://en.wikipedia.org/wiki/Tetrahymena_thermophila Tetrahymena thermophila]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a17 4a17], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a18 4a18], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a19 4a19], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a1a 4a1a], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a1b 4a1b], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a1c 4a1c], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a1d 4a1d] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4a1e 4a1e]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V8P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V8P FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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">X-ray diffraction, [[Resolution|Resolution]] 3.52&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4v8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v8p OCA], [http://pdbe.org/4v8p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v8p RCSB], [http://www.ebi.ac.uk/pdbsum/4v8p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v8p ProSAT]</span></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=4v8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v8p OCA], [https://pdbe.org/4v8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v8p RCSB], [https://www.ebi.ac.uk/pdbsum/4v8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v8p ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RL37_TETTS RL37_TETTS]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RL11_TETTH RL11_TETTH]] Binds to 5S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL40_TETTS RL40_TETTS]] 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-48-linked is involved in protein degradation via the proteasome. 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).  60S ribosomal protein L40: component of the 60S subunit of the ribosome. [[http://www.uniprot.org/uniprot/RL3_TETTH RL3_TETTH]] The L3 protein is a component of the large subunit of cytoplasmic ribosomes. [[http://www.uniprot.org/uniprot/IF6_TETTS IF6_TETTS]] Binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit to form the 80S initiation complex in the cytoplasm. May also be involved in ribosome biogenesis. [[http://www.uniprot.org/uniprot/RL5_TETTS RL5_TETTS]] This protein binds 5S RNA.  
[https://www.uniprot.org/uniprot/RL37_TETTS RL37_TETTS] Binds to the 23S rRNA.
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Tetrahymena thermophila]]
[[Category: Tetrahymena thermophila]]
[[Category: Arpagaus, S]]
[[Category: Arpagaus S]]
[[Category: Ban, N]]
[[Category: Ban N]]
[[Category: Klinge, S]]
[[Category: Klinge S]]
[[Category: Leibundgut, M]]
[[Category: Leibundgut M]]
[[Category: Voigts-Hoffmann, F]]
[[Category: Voigts-Hoffmann F]]
[[Category: Eif6]]
[[Category: Eukaryotic initiation factor 6]]
[[Category: Large ribosomal subunit]]
[[Category: Ribosomal protein]]
[[Category: Ribosome]]
[[Category: Rrna]]
[[Category: Translation]]

Latest revision as of 13:40, 10 January 2024

T.thermophila 60S ribosomal subunit in complex with initiation factor 6.T.thermophila 60S ribosomal subunit in complex with initiation factor 6.

Structural highlights

4v8p is a 40 chain structure with sequence from Tetrahymena thermophila. This structure supersedes the now removed PDB entries 4a17, 4a18, 4a19, 4a1a, 4a1b, 4a1c, 4a1d and 4a1e. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.52Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL37_TETTS Binds to the 23S rRNA.

Publication Abstract from PubMed

Protein synthesis in all organisms is catalyzed by ribosomes. In comparison to their prokaryotic counterparts, eukaryotic ribosomes are considerably larger and are subject to more complex regulation. The large ribosomal subunit (60S) catalyzes peptide bond formation and contains the nascent polypeptide exit tunnel. We present the structure of the 60S ribosomal subunit from Tetrahymena thermophila in complex with eukaryotic initiation factor 6 (eIF6), cocrystallized with the antibiotic cycloheximide (a eukaryotic-specific inhibitor of protein synthesis), at a resolution of 3.5 angstroms. The structure illustrates the complex functional architecture of the eukaryotic 60S subunit, which comprises an intricate network of interactions between eukaryotic-specific ribosomal protein features and RNA expansion segments. It reveals the roles of eukaryotic ribosomal protein elements in the stabilization of the active site and the extent of eukaryotic-specific differences in other functional regions of the subunit. Furthermore, it elucidates the molecular basis of the interaction with eIF6 and provides a structural framework for further studies of ribosome-associated diseases and the role of the 60S subunit in the initiation of protein synthesis.

Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6.,Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N Science. 2011 Nov 18;334(6058):941-8. Epub 2011 Nov 3. PMID:22052974[1]

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

See Also

References

  1. ↑ Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N. Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6. Science. 2011 Nov 18;334(6058):941-8. Epub 2011 Nov 3. PMID:22052974 doi:10.1126/science.1211204

4v8p, resolution 3.52Å

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