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Yorodumi- EMDB-50852: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-SIT... -
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| Title | CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA : LM32CS1C1 M2 OE MUTANT | |||||||||
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Keywords | CRYO-EM / LEISHMANIA MAJOR / 80S RIBOSOME / TRNA / MRNA / snoRNA / RIBOSOME | |||||||||
| Function / homology | Function and homology informationnuclear lumen / ciliary plasm / ciliary transition zone / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / rescue of stalled cytosolic ribosome ...nuclear lumen / ciliary plasm / ciliary transition zone / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / protein-RNA complex assembly / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / rescue of stalled cytosolic ribosome / protein kinase C binding / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / kinase activity / rRNA processing / ribosomal small subunit assembly / ribosome binding / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / nucleoplasm / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
| Biological species | Leishmania major strain Friedlin (eukaryote) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.25 Å | |||||||||
Authors | Rajan KS / Yonath A | |||||||||
| Funding support | European Union, 1 items
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Citation | Journal: Nat Commun / Year: 2026Title: A small nucleolar RNA dictates the structure and function of translating ribosomes in Leishmania. Authors: K Shanmugha Rajan / Saurav Aryal / Sharanya Murugeshan / Yinzhou Zhu / Anat Bashan / Mika Olami / Hava Madmoni / Yuko Nobe / Tirza Doniger / Smadar Cohen-Chalamish / Eric Prina / Pascale ...Authors: K Shanmugha Rajan / Saurav Aryal / Sharanya Murugeshan / Yinzhou Zhu / Anat Bashan / Mika Olami / Hava Madmoni / Yuko Nobe / Tirza Doniger / Smadar Cohen-Chalamish / Eric Prina / Pascale Pescher / Tom Beneke / Masato Taoka / Christopher L Holley / Ron Unger / Gerald F Späth / Ada Yonath / Shulamit Michaeli / ![]() Abstract: The most common rRNA modification is 2'-O-methylation. Here, we determine the landscape of 2'-O-methylation in Leishmania, a parasite that cycles between two different hosts, insect and mammalian. We ...The most common rRNA modification is 2'-O-methylation. Here, we determine the landscape of 2'-O-methylation in Leishmania, a parasite that cycles between two different hosts, insect and mammalian. We find two 2'-O-methylated positions that are differentially modified during the parasite's two life stages. The deposition of these modifications is guided by snoRNAs. When we perform cytosine base-editing of the snoRNA responsible for guiding one of the two stage-regulated modifications, Am479, we fail to detect ribosomes lacking this modification, suggesting that it is essential. To better understand the role of the snoRNA and its guided modification, we determine the cryo-EM structures of ribosomes from cells overexpressing the guiding snoRNA and compare them to ribosomes from the parental strain. We do not find structural changes around Am479 or in the small subunit rRNA, but observe a difference in H68 of the large subunit rRNA due to a second base-pairing interaction, suggesting a potential chaperone activity for the snoRNA. Based on these results, translatome and tRNA analysis, we propose a mechanism whereby changes in ribosome structure affect the release of specific tRNAs, which correlate with changes in translation of only a subset of mRNAs. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_50852.map.gz | 60.9 MB | EMDB map data format | |
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| Header (meta data) | emd-50852-v30.xml emd-50852.xml | 109.8 KB 109.8 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_50852_fsc.xml | 16.9 KB | Display | FSC data file |
| Images | emd_50852.png | 117.8 KB | ||
| Filedesc metadata | emd-50852.cif.gz | 21.8 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50852 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50852 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9fxoMC ![]() 56552 ![]() 56554 ![]() 56555 ![]() 56556 ![]() 56557 ![]() 57250 ![]() 8qhuC ![]() 8qieC 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_50852.map.gz / Format: CCP4 / Size: 421.9 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: 0.8245 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-SIT...
+Supramolecule #1: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-SIT...
+Macromolecule #1: LSUa_rRNA_chain_1
+Macromolecule #2: LSUb_rRNA_chain_2
+Macromolecule #3: SR1_chain_3
+Macromolecule #4: SR2_chain_4
+Macromolecule #5: SR4_chain_5
+Macromolecule #6: SR6_chain_6
+Macromolecule #7: 5.8S_rRNA_chain_7
+Macromolecule #8: 5S_rRNA_chain_8
+Macromolecule #51: SSU_rRNA_chain_S1
+Macromolecule #52: tRNA
+Macromolecule #53: tRNA
+Macromolecule #88: mRNA
+Macromolecule #9: Putative 60S ribosomal protein L2
+Macromolecule #10: Putative ribosomal protein L3
+Macromolecule #11: Putative ribosomal protein L1a
+Macromolecule #12: 60S ribosomal protein L11
+Macromolecule #13: Putative 60S ribosomal protein L9
+Macromolecule #14: Putative 60S ribosomal protein L6
+Macromolecule #15: 60S ribosomal protein L7a
+Macromolecule #16: Putative 60S ribosomal protein L13a
+Macromolecule #17: Putative 60S ribosomal protein L13
+Macromolecule #18: Putative 60S ribosomal protein L23
+Macromolecule #19: Putative 40S ribosomal protein L14
+Macromolecule #20: Putative 60S ribosomal protein L27A/L29
+Macromolecule #21: Ribosomal protein L15
+Macromolecule #22: Putative 60S ribosomal protein L10
+Macromolecule #23: Putative 60S ribosomal protein L5
+Macromolecule #24: 60S ribosomal protein L18
+Macromolecule #25: Putative 60S ribosomal protein L19
+Macromolecule #26: 60S ribosomal protein L18a
+Macromolecule #27: Putative 60S ribosomal protein L21
+Macromolecule #28: Putative 60S ribosomal protein L17
+Macromolecule #29: Putative 60S ribosomal protein L22
+Macromolecule #30: Putative 60S ribosomal protein L23a
+Macromolecule #31: Putative 60S ribosomal protein L26
+Macromolecule #32: Putative ribosomal protein L24
+Macromolecule #33: 60S ribosomal protein L27
+Macromolecule #34: Putative 60S ribosomal protein L28
+Macromolecule #35: Putative 60S ribosomal protein L35
+Macromolecule #36: 60S ribosomal protein L29
+Macromolecule #37: Putative 60S ribosomal protein L7
+Macromolecule #38: 60S ribosomal protein L30
+Macromolecule #39: Putative 60S ribosomal subunit protein L31
+Macromolecule #40: 60S ribosomal protein L32
+Macromolecule #41: Putative ribosomal protein l35a
+Macromolecule #42: Putative 60S ribosomal protein L34
+Macromolecule #43: Putative 60S Ribosomal protein L36
+Macromolecule #44: Ribosomal protein L37
+Macromolecule #45: Putative ribosomal protein L38
+Macromolecule #46: Putative 60S ribosomal protein L39
+Macromolecule #47: Ubiquitin-60S ribosomal protein L40
+Macromolecule #48: Ribosomal protein L41
+Macromolecule #49: 60S ribosomal protein L37a
+Macromolecule #50: Putative 60S ribosomal protein L44
+Macromolecule #54: 40S ribosomal protein S3a
+Macromolecule #55: 40S ribosomal protein SA
+Macromolecule #56: Putative 40S ribosomal protein S3
+Macromolecule #57: Putative 40S ribosomal protein S9
+Macromolecule #58: 40S ribosomal protein S4
+Macromolecule #59: 40S ribosomal protein S2
+Macromolecule #60: 40S ribosomal protein S6
+Macromolecule #61: 40S ribosomal protein S5
+Macromolecule #62: 40S ribosomal protein S7
+Macromolecule #63: Putative 40S ribosomal protein S15A
+Macromolecule #64: 40S ribosomal protein S8
+Macromolecule #65: Putative 40S ribosomal protein S16
+Macromolecule #66: Putative ribosomal protein S20
+Macromolecule #67: Putative 40S ribosomal protein S10
+Macromolecule #68: 40S ribosomal protein S14
+Macromolecule #69: Putative 40S ribosomal protein S23
+Macromolecule #70: 40S ribosomal protein S12
+Macromolecule #71: Putative 40S ribosomal protein S18
+Macromolecule #72: Putative ribosomal protein S29
+Macromolecule #73: Putative 40S ribosomal protein S13
+Macromolecule #74: Putative 40S ribosomal protein S11
+Macromolecule #75: Putative 40S ribosomal protein S17
+Macromolecule #76: Putative 40S ribosomal protein S15
+Macromolecule #77: 40S ribosomal protein S19-like protein
+Macromolecule #78: Putative 40S ribosomal protein S21
+Macromolecule #79: 40S ribosomal protein S24
+Macromolecule #80: 40S ribosomal protein S25
+Macromolecule #81: 40S ribosomal protein S26
+Macromolecule #82: Putative 40S ribosomal protein S27-1
+Macromolecule #83: Putative 40S ribosomal protein S33
+Macromolecule #84: 40S ribosomal protein S30
+Macromolecule #85: Ubiquitin-60S ribosomal protein L40
+Macromolecule #86: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #87: Putative RNA binding protein
+Macromolecule #89: SPERMIDINE
+Macromolecule #90: MAGNESIUM ION
+Macromolecule #91: SODIUM ION
+Macromolecule #92: POTASSIUM ION
+Macromolecule #93: 1,4-DIAMINOBUTANE
+Macromolecule #94: PAROMOMYCIN
+Macromolecule #95: ZINC ION
+Macromolecule #96: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.6 |
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| Grid | Model: Quantifoil R2/2 |
| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 0.92 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Keywords
Leishmania major strain Friedlin (eukaryote)
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Processing
FIELD EMISSION GUN


