[English] 日本語
Yorodumi- EMDB-15272: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : snoRNA MUTANT -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15272 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : snoRNA MUTANT | |||||||||
Map data | Merged Map | |||||||||
Sample |
| |||||||||
Keywords | CRYO-EM / LEISHMANIA MAJOR / 80S RIBOSOME snoRNA MUTANT / RIBOSOME | |||||||||
Function / homology | Function and homology information ciliary transition zone / nuclear lumen / ciliary plasm / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / 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) / rescue of stalled ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...ciliary transition zone / nuclear lumen / ciliary plasm / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / 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) / rescue of stalled ribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / small-subunit processome / protein kinase C binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / small ribosomal subunit / cytoplasmic translation / 5S rRNA binding / kinase activity / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / ribonucleoprotein complex / phosphorylation / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Leishmania major strain Friedlin (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.46 Å | |||||||||
Authors | Rajan KS / Yonath A / Bashan A | |||||||||
Funding support | Israel, 1 items
| |||||||||
Citation | Journal: Cell Rep / Year: 2024 Title: Structural and mechanistic insights into the function of Leishmania ribosome lacking a single pseudouridine modification Authors: Rajan KS / Aryal S / Hiregange DG / Bashan A / Madmoni H / Olami M / Doniger T / Cohen-Chalamish S / Pescher P / Taoka M / Nobe Y / Fedorenko A / Bose T / Zimermann E / Prina E / Aharon- ...Authors: Rajan KS / Aryal S / Hiregange DG / Bashan A / Madmoni H / Olami M / Doniger T / Cohen-Chalamish S / Pescher P / Taoka M / Nobe Y / Fedorenko A / Bose T / Zimermann E / Prina E / Aharon-Hefetz N / Pilpel Y / Isobe T / Unger R / Spath GF / Yonath A / Michaeli S | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_15272.map.gz | 56.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-15272-v30.xml emd-15272.xml | 109 KB 109 KB | Display Display | EMDB header |
Images | emd_15272.png | 77.2 KB | ||
Filedesc metadata | emd-15272.cif.gz | 20.5 KB | ||
Others | emd_15272_additional_1.map.gz emd_15272_half_map_1.map.gz emd_15272_half_map_2.map.gz | 66.2 MB 259.2 MB 259.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15272 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15272 | HTTPS FTP |
-Related structure data
Related structure data | 8a98MC 8ovjC 8rxhC 8rxxC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_15272.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Merged Map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Post processed consensus map
File | emd_15272_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Post processed consensus map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map 1
File | emd_15272_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map 2
File | emd_15272_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME snoRNA MUTANT
+Supramolecule #1: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME snoRNA MUTANT
+Macromolecule #1: Putative 40S ribosomal protein S15
+Macromolecule #2: 40S ribosomal protein S24
+Macromolecule #3: Putative 40S ribosomal protein S21
+Macromolecule #4: 40S ribosomal protein S19-like protein
+Macromolecule #5: Putative 40S ribosomal protein S17
+Macromolecule #6: Putative 40S ribosomal protein S11
+Macromolecule #7: Putative 40S ribosomal protein S13
+Macromolecule #8: Putative ribosomal protein S29
+Macromolecule #9: Putative 40S ribosomal protein S18
+Macromolecule #10: 40S ribosomal protein SA
+Macromolecule #11: Putative 40S ribosomal protein S3
+Macromolecule #12: Putative 40S ribosomal protein S9
+Macromolecule #13: 40S ribosomal protein S4
+Macromolecule #14: 40S ribosomal protein S8
+Macromolecule #16: Small ribosomal subunit protein RACK1
+Macromolecule #17: 40S ribosomal protein S25
+Macromolecule #18: Putative 40S ribosomal protein S27-1
+Macromolecule #19: 40S ribosomal protein S30
+Macromolecule #21: 40S ribosomal protein S12
+Macromolecule #22: Putative 40S ribosomal protein S23
+Macromolecule #23: 40S ribosomal protein S14
+Macromolecule #24: Putative 40S ribosomal protein S10
+Macromolecule #25: Putative 40S ribosomal protein S33
+Macromolecule #26: Putative ribosomal protein S20
+Macromolecule #27: Putative 40S ribosomal protein S16
+Macromolecule #28: Putative 40S ribosomal protein S15A
+Macromolecule #29: 40S ribosomal protein S7
+Macromolecule #30: 40S ribosomal protein S5
+Macromolecule #31: 40S ribosomal protein S6
+Macromolecule #32: 40S ribosomal protein S2
+Macromolecule #33: 40S ribosomal protein S3a
+Macromolecule #34: 40S ribosomal protein S26
+Macromolecule #35: Putative RNA binding protein
+Macromolecule #36: 60S ribosomal protein L32
+Macromolecule #37: 60S ribosomal protein L30
+Macromolecule #38: Putative 60S ribosomal protein L7
+Macromolecule #39: Putative 60S ribosomal protein L35
+Macromolecule #40: 60S ribosomal protein L29
+Macromolecule #45: Putative ribosomal protein L3
+Macromolecule #48: Putative 60S ribosomal protein L2
+Macromolecule #49: Putative 60S ribosomal protein L5
+Macromolecule #50: 60S ribosomal protein L7a
+Macromolecule #51: Putative 60S ribosomal protein L13a
+Macromolecule #52: Ribosomal protein L15
+Macromolecule #53: eL13_chain_I
+Macromolecule #54: 60S ribosomal protein L18
+Macromolecule #55: Putative 60S ribosomal protein L19
+Macromolecule #56: 60S ribosomal protein L18a
+Macromolecule #57: Putative 60S ribosomal protein L9
+Macromolecule #59: Putative 60S ribosomal protein L17
+Macromolecule #60: Putative 60S ribosomal protein L21
+Macromolecule #61: Putative 40S ribosomal protein L14
+Macromolecule #62: 60S ribosomal protein L11
+Macromolecule #63: Putative 60S ribosomal protein L27A/L29
+Macromolecule #64: 60S ribosomal protein L27
+Macromolecule #65: Putative 60S ribosomal protein L28
+Macromolecule #66: Putative 60S ribosomal protein L6
+Macromolecule #67: Putative 60S ribosomal protein L34
+Macromolecule #68: Putative ribosomal protein l35a
+Macromolecule #69: Putative 60S ribosomal protein L23
+Macromolecule #70: Putative 60S ribosomal protein L23a
+Macromolecule #71: Putative 60S ribosomal protein L26
+Macromolecule #72: Putative 60S ribosomal protein L22
+Macromolecule #73: Putative 60S Ribosomal protein L36
+Macromolecule #74: Putative 60S ribosomal protein L44
+Macromolecule #75: 60S ribosomal protein L37a
+Macromolecule #76: Putative ribosomal protein L24
+Macromolecule #77: Putative ribosomal protein L38
+Macromolecule #78: Putative 60S ribosomal protein L39
+Macromolecule #79: 60S ribosomal protein L41
+Macromolecule #80: Putative ribosomal protein L1a
+Macromolecule #82: Putative 60S ribosomal subunit protein L31
+Macromolecule #83: Ribosomal protein L37
+Macromolecule #15: E-site_tRNA_chain_S4
+Macromolecule #20: SSU_rRNA_chain_S1
+Macromolecule #41: LSUa_rRNA_chain_1
+Macromolecule #42: LSUb_rRNA_chain_2
+Macromolecule #43: SR2_chain_4
+Macromolecule #44: 5.8S_rRNA_chain_7
+Macromolecule #46: 5S_rRNA_chain_8
+Macromolecule #47: SR4_chain_5
+Macromolecule #58: SR6_chain_6
+Macromolecule #81: SR1_chain_3
+Macromolecule #84: MAGNESIUM ION
+Macromolecule #85: ZINC ION
+Macromolecule #86: SODIUM ION
+Macromolecule #87: POTASSIUM ION
+Macromolecule #88: water
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Component:
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 345376 |