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Structure paper

TitleVisualizing the translation landscape in human cells at high resolution.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 10757, Year 2025
Publish dateNov 28, 2025
AuthorsWei Zheng / Yuekang Zhang / Jimin Wang / Shuhui Wang / Pengxin Chai / Elizabeth J Bailey / Chenghao Zhu / Wangbiao Guo / Swapnil C Devarkar / Shenping Wu / Jianfeng Lin / Kai Zhang / Jun Liu / Ivan B Lomakin / Yong Xiong /
PubMed AbstractComprehensive 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 ...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 Å consensus structure of the human 80S ribosome and unveiled 23 functional states, nearly all better than 3 Å 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 NACβ 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.
External linksNat Commun / PubMed:41315256 / PubMed Central
MethodsEM (single particle)
Resolution2.19 - 3.91 Å
Structure data

71329

9p6z

EMDB-71329, PDB-9p6z:
In situ human P-Z state 80S ribosome
Method: EM (single particle) / Resolution: 2.97 Å

71331

9p72

EMDB-71331, PDB-9p72:
In situ human P-E state 80S ribosome
Method: EM (single particle) / Resolution: 2.8 Å

71332

9p73

EMDB-71332, PDB-9p73:
In situ human eEF2-A/P-P/E state 80S ribosome
Method: EM (single particle) / Resolution: 2.66 Å

71333

9p76

EMDB-71333, PDB-9p76:
In situ human eEF1A-A/T-P state 80S ribosome
Method: EM (single particle) / Resolution: 2.83 Å

71340

9p7f

EMDB-71340, PDB-9p7f:
In situ HHT and CHX treated A-P state 80S ribosome
Method: EM (single particle) / Resolution: 3.56 Å

71341

9p7g

EMDB-71341, PDB-9p7g:
In situ HHT and CHX treated A-P-Z state 80S ribosome
Method: EM (single particle) / Resolution: 3.54 Å

71342

9p7h

EMDB-71342, PDB-9p7h:
In situ HHT and CHX treated human eEF1A-A/T-P state 80S ribosome
Method: EM (single particle) / Resolution: 3.68 Å

71343

9p7i

EMDB-71343, PDB-9p7i:
In situ HHT and CHX treated human eEF1A-A/T-P-Z state 80S ribosome
Method: EM (single particle) / Resolution: 3.69 Å

71344

9p7j

EMDB-71344, PDB-9p7j:
In situ HHT and CHX treated human P state 80S ribosome
Method: EM (single particle) / Resolution: 3.91 Å

71345

9p7k

EMDB-71345, PDB-9p7k:
In situ human post eEF1A-A/T-P-E state 80S ribosome
Method: EM (single particle) / Resolution: 2.8 Å

71346

9p7l

EMDB-71346, PDB-9p7l:
In situ human Post-eEF1A-AT-P state 80S ribosome
Method: EM (single particle) / Resolution: 2.92 Å

71348

9p7n

EMDB-71348, PDB-9p7n:
In situ human Post-eEF1A-A/T-P-Z state 80S ribosome
Method: EM (single particle) / Resolution: 2.83 Å

71349

9p7o

EMDB-71349, PDB-9p7o:
In situ human AT-P-Z state ribosome
Method: EM (single particle) / Resolution: 2.65 Å

71355

9p7w

EMDB-71355, PDB-9p7w:
In situ human A-P state 80S ribosome
Method: EM (single particle) / Resolution: 2.93 Å

71356

9p7x

EMDB-71356, PDB-9p7x:
In situ human A-P-Z state 80S ribosome
Method: EM (single particle) / Resolution: 2.83 Å

71357

9p7y

EMDB-71357, PDB-9p7y:
In situ human A-P-E state 80S ribosome
Method: EM (single particle) / Resolution: 2.75 Å

71371

9p8b

EMDB-71371, PDB-9p8b:
In situ human eEF1A-A/T-P-E state 80S ribosome
Method: EM (single particle) / Resolution: 2.48 Å

71377

9p8h

EMDB-71377, PDB-9p8h:
In situ human A/P-P/E state 80S ribosome
Method: EM (single particle) / Resolution: 2.98 Å

71378

9p8i

EMDB-71378, PDB-9p8i:
In situ HHT and CHX treated human P-Z state 80S ribosome
Method: EM (single particle) / Resolution: 3.89 Å

71411

9p9h

EMDB-71411, PDB-9p9h:
In situ human unrotated hibernating with CCDC124 state 80S ribosome
Method: EM (single particle) / Resolution: 2.84 Å

71412

9p9i

EMDB-71412, PDB-9p9i:
In situ human unrotated hibernating without CCDC124 state 80S ribosome
Method: EM (single particle) / Resolution: 2.77 Å

71413

9p9j

EMDB-71413, PDB-9p9j:
In situ human 60S ribosome
Method: EM (single particle) / Resolution: 2.87 Å

71414

9p9k

EMDB-71414, PDB-9p9k:
In situ human 60S ribosome with EIF6
Method: EM (single particle) / Resolution: 2.96 Å

71435

9pa7

EMDB-71435, PDB-9pa7:
In situ human 80S consensus ribosome with EBP1
Method: EM (single particle) / Resolution: 2.67 Å

EMDB-71440: In situ human 80S ribosome (consensus map)
Method: EM (single particle) / Resolution: 2.19 Å

EMDB-71441: In situ human 80S ribosome (focused on 60S)
Method: EM (single particle) / Resolution: 2.2 Å

EMDB-71442: In situ human 80S ribosome (Focused on 40S body)
Method: EM (single particle) / Resolution: 2.51 Å

EMDB-71443: In situ human 80S ribosome (Focused on 40S head)
Method: EM (single particle) / Resolution: 2.64 Å

71477

9pbe

EMDB-71477, PDB-9pbe:
In situ human 80S ribosome (composite map)
Method: EM (single particle) / Resolution: 2.19 Å

71696

9pkg

EMDB-71696, PDB-9pkg:
In situ human P state 80S ribosome
Method: EM (single particle) / Resolution: 3.26 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-SPM:
SPERMINE

ChemComp-SPD:
SPERMIDINE

ChemComp-ZN:
Unknown entry

ChemComp-3HE:
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione

ChemComp-HMT:
(3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine

ChemComp-HOH:
WATER

ChemComp-K:
Unknown entry

ChemComp-PUT:
1,4-DIAMINOBUTANE

Source
  • homo sapiens (human)
KeywordsRIBOSOME / in situ / Ribsome

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