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Yorodumi- EMDB-16874: Structure of Candida albicans 80S ribosome in complex with mefloquine -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16874 | |||||||||||||||
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Title | Structure of Candida albicans 80S ribosome in complex with mefloquine | |||||||||||||||
Map data | Unfocused map | |||||||||||||||
Sample |
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Keywords | Candida albicans / ribosome / mefloquine | |||||||||||||||
Function / homology | Function and homology information filamentous growth of a population of unicellular organisms in response to neutral pH / cellular response to neutral pH / negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / filamentous growth of a population of unicellular organisms in response to biotic stimulus / filamentous growth of a population of unicellular organisms in response to starvation / yeast-form cell wall / GCN2-mediated signaling / regulation of cytoplasmic translation / hyphal cell wall ...filamentous growth of a population of unicellular organisms in response to neutral pH / cellular response to neutral pH / negative regulation of cell integrity MAPK cascade / positive regulation of conjugation with cellular fusion / filamentous growth of a population of unicellular organisms in response to biotic stimulus / filamentous growth of a population of unicellular organisms in response to starvation / yeast-form cell wall / GCN2-mediated signaling / regulation of cytoplasmic translation / hyphal cell wall / invasive growth in response to glucose limitation / negative regulation of p38MAPK cascade / filamentous growth / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding / mRNA destabilization / negative regulation of mRNA splicing, via spliceosome / G-protein alpha-subunit binding / protein-RNA complex assembly / ribosomal subunit export from nucleus / positive regulation of autophagy / translation regulator activity / maturation of LSU-rRNA / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to starvation / rescue of stalled ribosome / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / large ribosomal subunit / extracellular vesicle / ribosome biogenesis / ribosome binding / 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 / cell adhesion / rRNA binding / ribosome / structural constituent of ribosome / protein ubiquitination / translation / ribonucleoprotein complex / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / ubiquitin protein ligase binding / cell surface / RNA binding / zinc ion binding / extracellular region / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Candida albicans (yeast) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Kolosova O / Zgadzay Y / Stetsenko A / Guskov A / Yusupov M | |||||||||||||||
Funding support | France, Russian Federation, 4 items
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Citation | Journal: To Be Published Title: Drug-induced rotational movement of the ribosome is a key factor for read-through enhancement Authors: Kolosova O / Zgadzay Y / Yusupov M | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16874.map.gz | 242.1 MB | EMDB map data format | |
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Header (meta data) | emd-16874-v30.xml emd-16874.xml | 98.2 KB 98.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16874_fsc.xml | 13.9 KB | Display | FSC data file |
Images | emd_16874.png | 149.3 KB | ||
Filedesc metadata | emd-16874.cif.gz | 18.6 KB | ||
Others | emd_16874_half_map_1.map.gz emd_16874_half_map_2.map.gz | 261.8 MB 261.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16874 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16874 | HTTPS FTP |
-Validation report
Summary document | emd_16874_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_16874_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_16874_validation.xml.gz | 23 KB | Display | |
Data in CIF | emd_16874_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16874 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16874 | HTTPS FTP |
-Related structure data
Related structure data | 8ogjMC 8cq7C 8cqwC 8creC 8oeqC 8oh6C 8oi5C 8oj3C 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_16874.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Unfocused map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.02 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_16874_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_16874_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Candida albicans 80S ribosome in complex with mefloquine
+Supramolecule #1: Candida albicans 80S ribosome in complex with mefloquine
+Macromolecule #1: 25S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 5.8S ribosomal RNA
+Macromolecule #4: Mixture of endogenous E-tRNAs
+Macromolecule #46: 18S ribosomal RNA
+Macromolecule #5: 60S ribosomal protein L2-B
+Macromolecule #6: 60S ribosomal protein L3
+Macromolecule #7: 60S ribosomal protein L4-B
+Macromolecule #8: 60S ribosomal protein L5
+Macromolecule #9: 60S ribosomal protein L6
+Macromolecule #10: 60S ribosomal protein L7-A
+Macromolecule #11: 60S ribosomal protein L8
+Macromolecule #12: 60S ribosomal protein L9-B
+Macromolecule #13: 60S ribosomal protein L10
+Macromolecule #14: 60S ribosomal protein L11-B
+Macromolecule #15: 60S ribosomal protein L13
+Macromolecule #16: 60S ribosomal protein L14-B
+Macromolecule #17: 60S ribosomal protein L15-A
+Macromolecule #18: Ribosomal protein L13
+Macromolecule #19: Ribosomal protein L22
+Macromolecule #20: 60S ribosomal protein L18-A
+Macromolecule #21: 60S ribosomal protein L19-A
+Macromolecule #22: 60S ribosomal protein L20
+Macromolecule #23: 60S ribosomal protein L21-A
+Macromolecule #24: 60S ribosomal protein L22-B
+Macromolecule #25: 60S ribosomal protein L23-A
+Macromolecule #26: 60S ribosomal protein L24-A
+Macromolecule #27: 60S ribosomal protein L25
+Macromolecule #28: Ribosomal protein L24
+Macromolecule #29: 60S ribosomal protein L27
+Macromolecule #30: 60S ribosomal protein L28
+Macromolecule #31: 60S ribosomal protein L29
+Macromolecule #32: 60S ribosomal protein L30
+Macromolecule #33: 60S ribosomal protein L31-B
+Macromolecule #34: 60S ribosomal protein L32
+Macromolecule #35: 60S ribosomal protein L33-A
+Macromolecule #36: 60S ribosomal protein L34-B
+Macromolecule #37: Ribosomal protein L29
+Macromolecule #38: 60S ribosomal protein L36
+Macromolecule #39: 60S ribosomal protein L37-B
+Macromolecule #40: 60S ribosomal protein L38
+Macromolecule #41: 60S ribosomal protein L39
+Macromolecule #42: 60S ribosomal protein L40-B
+Macromolecule #43: 60S ribosomal protein L41
+Macromolecule #44: 60S ribosomal protein L42-B
+Macromolecule #45: 60S ribosomal protein L43-A
+Macromolecule #47: 40S ribosomal protein S0
+Macromolecule #48: 40S ribosomal protein S1
+Macromolecule #49: Ribosomal protein S5
+Macromolecule #50: Ribosomal protein S3
+Macromolecule #51: 40S ribosomal protein S4
+Macromolecule #52: Ribosomal protein S7
+Macromolecule #53: 40S ribosomal protein S6
+Macromolecule #54: 40S ribosomal protein S7
+Macromolecule #55: 40S ribosomal protein S8
+Macromolecule #56: Ribosomal protein S4
+Macromolecule #57: 40S ribosomal protein S10-A
+Macromolecule #58: 40S ribosomal protein S11A
+Macromolecule #59: 40S ribosomal protein S12
+Macromolecule #60: 40S ribosomal protein S13
+Macromolecule #61: 40S ribosomal protein S14-A
+Macromolecule #62: 40S ribosomal protein S15
+Macromolecule #63: 40S ribosomal protein S16
+Macromolecule #64: 40S ribosomal protein S17-B
+Macromolecule #65: 40S ribosomal protein S18-B
+Macromolecule #66: 40S ribosomal protein S19-A
+Macromolecule #67: Ribosomal protein S10
+Macromolecule #68: 40S ribosomal protein S21
+Macromolecule #69: 40S ribosomal protein S22-A
+Macromolecule #70: Ribosomal protein S23 (S12)
+Macromolecule #71: 40S ribosomal protein S24
+Macromolecule #72: 40S ribosomal protein S25
+Macromolecule #73: 40S ribosomal protein S26
+Macromolecule #74: 40S ribosomal protein S27
+Macromolecule #75: 40S ribosomal protein S28-B
+Macromolecule #76: 40S ribosomal protein S29A
+Macromolecule #77: 40S ribosomal protein S30
+Macromolecule #78: Ubiquitin-40S ribosomal protein S31 fusion protein
+Macromolecule #79: Guanine nucleotide-binding protein subunit beta-like protein
+Macromolecule #80: (11R,12S)- Mefloquine
+Macromolecule #81: SPERMINE (FULLY PROTONATED FORM)
+Macromolecule #82: MAGNESIUM ION
+Macromolecule #83: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.3 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 16.0 µm / Nominal defocus min: 5.0 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-8ogj: |