+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15124 | |||||||||
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Title | CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE | |||||||||
Map data | Merged map | |||||||||
Sample |
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Keywords | CRYO-EM LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE / 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) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome ...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) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / kinase activity / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / positive regulation of protein phosphorylation / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Leishmania major strain Friedlin (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.89 Å | |||||||||
Authors | Rajan KS / Yonath A / Bashan A | |||||||||
Funding support | Israel, 1 items
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Citation | Journal: To Be Published Title: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : WILD TYPE Authors: Rajan KS | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15124.map.gz | 52.7 MB | EMDB map data format | |
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Header (meta data) | emd-15124-v30.xml emd-15124.xml | 106.9 KB 106.9 KB | Display Display | EMDB header |
Images | emd_15124.png | 71.6 KB | ||
Filedesc metadata | emd-15124.cif.gz | 20.2 KB | ||
Others | emd_15124_additional_1.map.gz emd_15124_half_map_1.map.gz emd_15124_half_map_2.map.gz | 50.1 MB 260.6 MB 260.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15124 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15124 | HTTPS FTP |
-Validation report
Summary document | emd_15124_validation.pdf.gz | 1014.6 KB | Display | EMDB validaton report |
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Full document | emd_15124_full_validation.pdf.gz | 1014.1 KB | Display | |
Data in XML | emd_15124_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | emd_15124_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15124 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15124 | HTTPS FTP |
-Related structure data
Related structure data | 8a3wMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15124.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Merged map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Post processed consensus map
File | emd_15124_additional_1.map | ||||||||||||
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Annotation | Post processed consensus map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_15124_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_15124_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE
+Supramolecule #1: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE
+Macromolecule #1: Putative 40S ribosomal protein S9
+Macromolecule #2: 40S ribosomal protein S4
+Macromolecule #3: 40S ribosomal protein S2
+Macromolecule #4: 40S ribosomal protein S6
+Macromolecule #5: 40S ribosomal protein S5
+Macromolecule #6: 40S ribosomal protein S7
+Macromolecule #7: Putative 40S ribosomal protein S15A
+Macromolecule #8: 40S ribosomal protein S8
+Macromolecule #9: Putative 40S ribosomal protein S16
+Macromolecule #10: Putative ribosomal protein S20
+Macromolecule #11: Putative 40S ribosomal protein S10
+Macromolecule #12: 40S ribosomal protein S14
+Macromolecule #13: Putative 40S ribosomal protein S23
+Macromolecule #14: Putative 40S ribosomal protein S18
+Macromolecule #15: Putative ribosomal protein S29
+Macromolecule #16: Putative 40S ribosomal protein S13
+Macromolecule #17: Putative 40S ribosomal protein S11
+Macromolecule #18: Putative 40S ribosomal protein S17
+Macromolecule #19: Putative 40S ribosomal protein S15
+Macromolecule #20: 40S ribosomal protein S19-like protein
+Macromolecule #21: Putative 40S ribosomal protein S21
+Macromolecule #22: 40S ribosomal protein S24
+Macromolecule #23: 40S ribosomal protein S25
+Macromolecule #24: 40S ribosomal protein S26
+Macromolecule #25: Putative 40S ribosomal protein S27-1
+Macromolecule #26: Putative 40S ribosomal protein S33
+Macromolecule #27: 40S ribosomal protein S30
+Macromolecule #28: Small ribosomal subunit protein RACK1
+Macromolecule #30: 40S ribosomal protein S3a
+Macromolecule #31: 40S ribosomal protein SA
+Macromolecule #32: Putative 40S ribosomal protein S3
+Macromolecule #33: Putative RNA binding protein
+Macromolecule #43: Putative ribosomal protein L3
+Macromolecule #44: Putative ribosomal protein L1a
+Macromolecule #45: Putative 60S ribosomal protein L2
+Macromolecule #46: uL30_chain_c
+Macromolecule #47: Putative 60S ribosomal protein L5
+Macromolecule #48: Ribosomal protein L15
+Macromolecule #49: Putative 60S ribosomal protein L13a
+Macromolecule #50: 60S ribosomal protein L7a
+Macromolecule #51: 60S ribosomal protein L18
+Macromolecule #52: 60S ribosomal protein L18a
+Macromolecule #53: eL13_chain_I
+Macromolecule #54: Putative 60S ribosomal protein L19
+Macromolecule #55: Putative 60S ribosomal protein L17
+Macromolecule #56: Putative 60S ribosomal protein L21
+Macromolecule #57: Putative 60S ribosomal protein L27A/L29
+Macromolecule #58: Putative 60S ribosomal protein L6
+Macromolecule #59: Putative 60S ribosomal protein L9
+Macromolecule #60: 60S ribosomal protein L27
+Macromolecule #61: 60S ribosomal protein L32
+Macromolecule #62: Putative ribosomal protein l35a
+Macromolecule #63: Putative 60S ribosomal protein L35
+Macromolecule #64: Putative 60S ribosomal protein L23
+Macromolecule #65: Putative 60S ribosomal protein L26
+Macromolecule #66: Putative 60S ribosomal protein L23a
+Macromolecule #67: Putative 60S ribosomal protein L34
+Macromolecule #68: Putative 60S ribosomal protein L28
+Macromolecule #69: Putative 40S ribosomal protein L14
+Macromolecule #70: Ribosomal protein L37
+Macromolecule #71: Putative 60S Ribosomal protein L36
+Macromolecule #72: Putative 60S ribosomal protein L22
+Macromolecule #73: Putative 60S ribosomal protein L44
+Macromolecule #74: 60S ribosomal protein L37a
+Macromolecule #75: 60S ribosomal protein L11
+Macromolecule #76: 60S ribosomal protein L30
+Macromolecule #77: Putative ribosomal protein L24
+Macromolecule #78: 60S ribosomal protein L29
+Macromolecule #79: Putative ribosomal protein L38
+Macromolecule #80: Putative 60S ribosomal protein L39
+Macromolecule #81: 60S ribosomal protein L41
+Macromolecule #82: Putative 60S ribosomal subunit protein L31
+Macromolecule #29: SSU_rRNA_chain_S1
+Macromolecule #34: E-site_tRNA_chain_S4
+Macromolecule #35: 5S_rRNA_chain_8
+Macromolecule #36: SR6_chain_6
+Macromolecule #37: LSUb_rRNA_chain_2
+Macromolecule #38: 5.8S_rRNA_chain_7
+Macromolecule #39: SR4_chain_5
+Macromolecule #40: SR2_chain_4
+Macromolecule #41: SR1_chain_3
+Macromolecule #42: LSUa_rRNA_chain_1
+Macromolecule #83: MAGNESIUM ION
+Macromolecule #84: SODIUM ION
+Macromolecule #85: ZINC ION
+Macromolecule #86: POTASSIUM ION
+Macromolecule #87: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-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: 1.0 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: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 742580 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |