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Yorodumi- EMDB-54790: Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subun... -
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Open data
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Basic information
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| Title | Cryo-EM structure of the Arabidopsis thaliana 40S ribosomal subunit (Head) | ||||||||||||
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Keywords | Ribosomal 40S subunit -Head region / RIBOSOME | ||||||||||||
| Function / homology | Function and homology informationplant-type cell wall / plasmodesma / plant-type vacuole / vacuole / plastid / cytosolic ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / translational initiation ...plant-type cell wall / plasmodesma / plant-type vacuole / vacuole / plastid / cytosolic ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / translational initiation / peroxisome / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / defense response to bacterium / rRNA binding / structural constituent of ribosome / ribosome / translation / mRNA binding / nucleolus / endoplasmic reticulum / mitochondrion / RNA binding / zinc ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||
| Biological species | ![]() | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Sudeep K / Lu X / Paatero AO / Ruonala R / Tranter D / Guryanov S / Rehan S / Hellmann E / Haakonsson A / Butcher SJ ...Sudeep K / Lu X / Paatero AO / Ruonala R / Tranter D / Guryanov S / Rehan S / Hellmann E / Haakonsson A / Butcher SJ / Huiskonen JT / Kajander T / Helariutta Y / Paavilainen VO | ||||||||||||
| Funding support | United States, Finland, 3 items
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Citation | Journal: Structure / Year: 2026Title: Cryo-EM structure of the Arabidopsisthaliana ribosome in translating and non-translating states. Authors: Sudeep Karki / Xun Lu / Anja O Paatero / Raili Ruonala / Dale Tranter / Sergey Guryanov / Shahid Rehan / Eva Hellmann / Anders Haakonsson / Sarah J Butcher / Juha T Huiskonen / Tommi ...Authors: Sudeep Karki / Xun Lu / Anja O Paatero / Raili Ruonala / Dale Tranter / Sergey Guryanov / Shahid Rehan / Eva Hellmann / Anders Haakonsson / Sarah J Butcher / Juha T Huiskonen / Tommi Kajander / Yrjö Helariutta / Ville O Paavilainen / ![]() Abstract: Translational control of mRNA expression underpins much of post-transcriptional gene expression driving developmental processes in eukaryotes. How ribosomal mRNA translation is executed in plants may ...Translational control of mRNA expression underpins much of post-transcriptional gene expression driving developmental processes in eukaryotes. How ribosomal mRNA translation is executed in plants may be especially important for adapting to an ever-changing environment. Arabidopsis thaliana is the main genetic model organism in plant science, yet structural insights into developmental processes where ribosomal gene expression plays important roles currently remain lacking. Here, we present cryoelectron microscopy (cryo-EM) structures of the Arabidopsis cytosolic ribosome in both translating and non-translating states, which together provide new structural details into how translation of cytosolic mRNAs is coordinated. Our structures reveal detailed information on the interactions of tRNAs, mRNA, and the nascent polypeptide with subunits of the actively translating 80S ribosome and the role of ribosomal RNA methylation in stabilizing ribosomal subunits. The structures provide a foundation for interpreting the functional effects of many mutations of ribosomal proteins affecting phenotypic effects for plant tissue development. | ||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_54790.map.gz | 301.6 MB | EMDB map data format | |
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| Header (meta data) | emd-54790-v30.xml emd-54790.xml | 31.7 KB 31.7 KB | Display Display | EMDB header |
| Images | emd_54790.png | 62.2 KB | ||
| Filedesc metadata | emd-54790.cif.gz | 8.1 KB | ||
| Others | emd_54790_half_map_1.map.gz emd_54790_half_map_2.map.gz | 322.9 MB 322.9 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-54790 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-54790 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9sdqMC ![]() 9scuC ![]() 9sdpC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_54790.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #2
| File | emd_54790_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_54790_half_map_2.map | ||||||||||||
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Sample components
+Entire : 40S SSU Arabidopsis (root) ribosome complex
+Supramolecule #1: 40S SSU Arabidopsis (root) ribosome complex
+Macromolecule #1: RNA (500-MER)
+Macromolecule #2: Small ribosomal subunit protein uS3z
+Macromolecule #3: Small ribosomal subunit protein uS7z
+Macromolecule #4: Small ribosomal subunit protein uS19x
+Macromolecule #5: Small ribosomal subunit protein uS9z
+Macromolecule #6: Small ribosomal subunit protein uS13z/uS13y/uS13x
+Macromolecule #7: Small ribosomal subunit protein eS19x
+Macromolecule #8: Small ribosomal subunit protein uS10z/uS10x
+Macromolecule #9: Small ribosomal subunit protein eS28x
+Macromolecule #10: Small ribosomal subunit protein uS14z/uS14y/uS14x
+Macromolecule #11: Small ribosomal subunit protein eS25y
+Macromolecule #12: Small ribosomal subunit protein eS10x
+Macromolecule #13: Small ribosomal subunit protein eS17w
+Macromolecule #14: POTASSIUM ION
+Macromolecule #15: MAGNESIUM ION
+Macromolecule #16: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | tissue |
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Sample preparation
| Buffer | pH: 7.4 Details: 50 mM Hepes, pH 7.4, 5 mM MgAc, 100 mM KAc, pH 7.5, 1 mM DTT, Complete protease inhibitor |
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| Grid | Model: Quantifoil / Material: COPPER |
| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 24.512 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 10500 |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Authors
United States,
Finland, 3 items
Citation








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Processing
FIELD EMISSION GUN
