6mtd
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel)== | |
| + | <SX load='6mtd' size='340' side='right' viewer='molstar' caption='[[6mtd]], [[Resolution|resolution]] 3.30Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6mtd]] 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=6MTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MTD FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.3Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4AC:N(4)-ACETYLCYTIDINE-5-MONOPHOSPHATE'>4AC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=B8H:[(2~{R},3~{S},4~{R},5~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>B8H</scene>, <scene name='pdbligand=B8K:[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-ethanoyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>B8K</scene>, <scene name='pdbligand=B8N:(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic+acid'>B8N</scene>, <scene name='pdbligand=B8Q:[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-3-methyl-2-oxidanylidene-4~{H}-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>B8Q</scene>, <scene name='pdbligand=B8T:[(2~{R},3~{S},4~{R},5~{R})-5-[4-(methylamino)-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>B8T</scene>, <scene name='pdbligand=B8W:[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-methoxy-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>B8W</scene>, <scene name='pdbligand=B9B:[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-propoxy-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>B9B</scene>, <scene name='pdbligand=B9H:[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-3-propyl-4~{H}-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl+dihydrogen+phosphate'>B9H</scene>, <scene name='pdbligand=BGH:[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-ethanoyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl+dihydrogen+phosphate'>BGH</scene>, <scene name='pdbligand=DDE:{3-[4-(2-AMINO-2-CARBOXY-ETHYL)-1H-IMIDAZOL-2-YL]-1-CARBAMOYL-PROPYL}-TRIMETHYL-AMMONIUM'>DDE</scene>, <scene name='pdbligand=E6G:[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-ethoxy-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>E6G</scene>, <scene name='pdbligand=E7G:[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-ethyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>E7G</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=I4U:[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanylidene-4-propan-2-yloxy-pyrimidin-1-yl)oxolan-2-yl]methyl+dihydrogen+phosphate'>I4U</scene>, <scene name='pdbligand=M7A:[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-7-methyl-8~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>M7A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MHG:[(2~{R},3~{S},4~{R},5~{R})-5-[2-(methylamino)-7-[(3~{S})-3-methylpentyl]-6-oxidanylidene-1,8-dihydropurin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>MHG</scene>, <scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=P4U:[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanylidene-4-propoxy-pyrimidin-1-yl)oxolan-2-yl]methyl+dihydrogen+phosphate'>P4U</scene>, <scene name='pdbligand=P7G:[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-7-propyl-3,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>P7G</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</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'>[https://proteopedia.org/fgij/fg.htm?mol=6mtd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mtd OCA], [https://pdbe.org/6mtd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mtd RCSB], [https://www.ebi.ac.uk/pdbsum/6mtd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mtd ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/RL8_RABIT RL8_RABIT] Component of the large ribosomal subunit (PubMed:25601755, PubMed:26245381, PubMed:27863242, PubMed:30517857). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:25601755, PubMed:26245381, PubMed:27863242, PubMed:30517857).<ref>PMID:25601755</ref> <ref>PMID:26245381</ref> <ref>PMID:27863242</ref> <ref>PMID:30517857</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression. | ||
| - | + | Structures of translationally inactive mammalian ribosomes.,Brown A, Baird MR, Yip MC, Murray J, Shao S Elife. 2018 Oct 24;7. pii: 40486. doi: 10.7554/eLife.40486. PMID:30355441<ref>PMID:30355441</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 6mtd" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | |
| - | [[Category: | + | ==See Also== |
| - | [[Category: | + | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| - | [[Category: | + | *[[3D sructureseceptor for activated protein kinase C 1|3D sructureseceptor for activated protein kinase C 1]] |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </SX> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Oryctolagus cuniculus]] | ||
| + | [[Category: Baird MR]] | ||
| + | [[Category: Brown A]] | ||
| + | [[Category: Murray J]] | ||
| + | [[Category: Shao S]] | ||
| + | [[Category: Yip MCJ]] | ||
Current revision
Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel)
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