9p9k: Difference between revisions

Latest revision as of 14:17, 1 July 2026

In situ human 60S ribosome with EIF6

Structural highlights

9p9k is a 10 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.96Å
Ligands:	1MA, 5MC, 6MZ, A2M, MG, OMC, OMG, OMU, PSU, SPD, SPM, UR3, UY1, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL8_HUMAN

Publication Abstract from PubMed

Comprehensive in situ structures of macromolecules can transform our understanding of biology and advance human health. Here, we map protein synthesis inside human cells in detail by combining automated cryo-focused ion beam (FIB) milling and in situ single-particle cryo electron microscopy (cryo-EM). With this in situ cryo-EM approach, we resolved a 2.2 A consensus structure of the human 80S ribosome and unveiled 23 functional states, nearly all better than 3 A resolution. Compared to in vitro studies, we observed variations in ribosome structures, distinct environments of ion and polyamine binding, and associated proteins such as EDF1 and NACbeta that are typically not enriched with purified ribosomes. We also detected additional peptide-related density features on the ribosome and visualized ribosome-ribosome interactions in helical polysomes. Finally, high-resolution structures from cells treated with homoharringtonine and cycloheximide revealed a distinct translational landscape and a spermidine that interacts with cycloheximide at the E site, one of the numerous polyamines that also bind native ribosomes. These results underscore the value of high-resolution in situ studies in the native environment.

Visualizing the translation landscape in human cells at high resolution.,Zheng W, Zhang Y, Wang J, Wang S, Chai P, Bailey EJ, Zhu C, Guo W, Devarkar SC, Wu S, Lin J, Zhang K, Liu J, Lomakin IB, Xiong Y Nat Commun. 2025 Nov 28;16(1):10757. doi: 10.1038/s41467-025-65795-9. PMID:41315256^[1]

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

References

↑ Zheng W, Zhang Y, Wang J, Wang S, Chai P, Bailey EJ, Zhu C, Guo W, Devarkar SC, Wu S, Lin J, Zhang K, Liu J, Lomakin IB, Xiong Y. Visualizing the translation landscape in human cells at high resolution. Nat Commun. 2025 Nov 28;16(1):10757. PMID:41315256 doi:10.1038/s41467-025-65795-9

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OCA

[1] Zheng W, Zhang Y, Wang J, Wang S, Chai P, Bailey EJ, Zhu C, Guo W, Devarkar SC, Wu S, Lin J, Zhang K, Liu J, Lomakin IB, Xiong Y. Visualizing the translation landscape in human cells at high resolution. Nat Commun. 2025 Nov 28;16(1):10757. PMID:41315256 doi:10.1038/s41467-025-65795-9

[1]

@@ Line 5: / Line 5: @@
 <table><tr><td colspan='2'>[[9p9k]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9P9K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9P9K 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]] 2.96&#8491;</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=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=UY1:[(2~{R},3~{R},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)-1~{H}-pyrimidin-5-yl]-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl+dihydrogen+phosphate'>UY1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=UY1:(1S)-1,4-anhydro-1-[(5S)-2,6-dioxo-1,2,5,6-tetrahydropyrimidin-5-yl]-2-O-methyl-5-O-phosphono-D-ribitol'>UY1</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=9p9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9p9k OCA], [https://pdbe.org/9p9k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9p9k RCSB], [https://www.ebi.ac.uk/pdbsum/9p9k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9p9k ProSAT]</span></td></tr>
 </table>

9p9k: Difference between revisions

Latest revision as of 14:17, 1 July 2026

In situ human 60S ribosome with EIF6

Structural highlights

Function

Publication Abstract from PubMed

References

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