+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17653 | |||||||||
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Title | Mouse RPL39L integrated into the yeast 60S ribosomal subunit | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RPL39 / RPL39L / ribosomal protein / protein exit tunnel / RIBOSOME | |||||||||
Function / homology | Function and homology information Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide ...Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / translational termination / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / macroautophagy / maintenance of translational fidelity / ribosomal large subunit assembly / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / spermatogenesis / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / RNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.15 Å | |||||||||
Authors | Rabl J / Banerjee A / Boehringer D / Zavolan M | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography. Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams / Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17653.map.gz | 779 MB | EMDB map data format | |
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Header (meta data) | emd-17653-v30.xml emd-17653.xml | 64.5 KB 64.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17653_fsc.xml | 19.7 KB | Display | FSC data file |
Images | emd_17653.png | 153.5 KB | ||
Masks | emd_17653_msk_1.map | 824 MB | Mask map | |
Filedesc metadata | emd-17653.cif.gz | 14 KB | ||
Others | emd_17653_half_map_1.map.gz emd_17653_half_map_2.map.gz | 763.8 MB 763.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17653 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17653 | HTTPS FTP |
-Validation report
Summary document | emd_17653_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_17653_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_17653_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | emd_17653_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17653 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17653 | HTTPS FTP |
-Related structure data
Related structure data | 8pfrMC M: atomic model generated by this map C: citing same article (ref.) |
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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_17653.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17653_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17653_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17653_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mouse RPL39L in yeast 60S ribosomal subunit
+Supramolecule #1: Mouse RPL39L in yeast 60S ribosomal subunit
+Macromolecule #1: 25S rRNA
+Macromolecule #38: 5.8S rRNA
+Macromolecule #42: 5S rRNA
+Macromolecule #2: 60S ribosomal protein L32
+Macromolecule #3: 60S ribosomal protein L8-A
+Macromolecule #4: 60S ribosomal protein L22-A
+Macromolecule #5: 60S ribosomal protein L26-A
+Macromolecule #6: 60S ribosomal protein L2-A
+Macromolecule #7: 60S ribosomal protein L39-like
+Macromolecule #8: 60S ribosomal protein L23-A
+Macromolecule #9: 60S ribosomal protein L13-A
+Macromolecule #10: 60S ribosomal protein L33-A
+Macromolecule #11: 60S ribosomal protein L9-A
+Macromolecule #12: 60S ribosomal protein L24-A
+Macromolecule #13: 60S ribosomal protein L27-A
+Macromolecule #14: 60S ribosomal protein L3
+Macromolecule #15: Ubiquitin-60S ribosomal protein L40
+Macromolecule #16: 60S ribosomal protein L25
+Macromolecule #17: 60S ribosomal protein L14-A
+Macromolecule #18: 60S ribosomal protein L34-A
+Macromolecule #19: 60S ribosomal protein L10
+Macromolecule #20: 60S ribosomal protein L4-A
+Macromolecule #21: 60S ribosomal protein L28
+Macromolecule #22: 60S ribosomal protein L35-A
+Macromolecule #23: 60S ribosomal protein L42-A
+Macromolecule #24: 60S ribosomal protein L5
+Macromolecule #25: 60S ribosomal protein L15-A
+Macromolecule #26: 60S ribosomal protein L36-A
+Macromolecule #27: 60S ribosomal protein L11-A
+Macromolecule #28: 60S ribosomal protein L6-A
+Macromolecule #29: 60S ribosomal protein L29
+Macromolecule #30: 60S ribosomal protein L37-A
+Macromolecule #31: 60S ribosomal protein L43-A
+Macromolecule #32: 60S ribosomal protein L7-A
+Macromolecule #33: 60S ribosomal protein L16-A
+Macromolecule #34: 60S ribosomal protein L38
+Macromolecule #35: 60S ribosomal protein L17-A
+Macromolecule #36: 60S ribosomal protein L30
+Macromolecule #37: 60S ribosomal protein L18-A
+Macromolecule #39: 60S ribosomal protein L19-A
+Macromolecule #40: 60S ribosomal protein L31-A
+Macromolecule #41: 60S ribosomal protein L20-A
+Macromolecule #43: 60S ribosomal protein L21-A
+Macromolecule #44: MAGNESIUM ION
+Macromolecule #45: CHLORIDE ION
+Macromolecule #46: SPERMINE
+Macromolecule #47: SPERMIDINE
+Macromolecule #48: ZINC ION
+Macromolecule #49: 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 Details: 50mM Hepes pH 7.6, 200 mM KCl, 10 mM MgCl2, 5 mM EDTA, 2 mM DTT |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Details: 15mA |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 30s pre-blot incubation. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |