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Open data
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Basic information
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Title | Mouse RPL39 integrated into the yeast 60S ribosomal subunit | |||||||||
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![]() | 60S ribosomal subunit / protein exit tunnel / RPL39 / RPL39L / RIBOSOME | |||||||||
Function / homology | ![]() 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 / 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 | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.15 Å | |||||||||
![]() | Rabl J / Banerjee A / Boehringer D / Zavolan M | |||||||||
Funding support | ![]()
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![]() | 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 | ![]() | 775.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 61.6 KB 61.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 19.7 KB | Display | ![]() |
Images | ![]() | 149.6 KB | ||
Masks | ![]() | 824 MB | ![]() | |
Filedesc metadata | ![]() | 13.5 KB | ||
Others | ![]() ![]() | 764 MB 763.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 37.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p8nMC ![]() 8p8mC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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Density Histograms |
-Half map: #2
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Projections & Slices |
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
+Entire : Mouse RPL39 integrated into yeast 60S ribosomal subunit
+Supramolecule #1: Mouse RPL39 integrated into yeast 60S ribosomal subunit
+Macromolecule #1: Large ribosomal subunit protein eL39
+Macromolecule #2: 60S ribosomal protein L7-A
+Macromolecule #3: 60S ribosomal protein L25
+Macromolecule #4: 60S ribosomal protein L38
+Macromolecule #6: 60S ribosomal protein L8-A
+Macromolecule #7: 60S ribosomal protein L26-A
+Macromolecule #8: Ubiquitin-60S ribosomal protein L40
+Macromolecule #9: 60S ribosomal protein L13-A
+Macromolecule #10: 60S ribosomal protein L9-A
+Macromolecule #11: 60S ribosomal protein L27-A
+Macromolecule #12: 60S ribosomal protein L42-A
+Macromolecule #13: 60S ribosomal protein L14-A
+Macromolecule #14: 60S ribosomal protein L10
+Macromolecule #15: 60S ribosomal protein L28
+Macromolecule #16: 60S ribosomal protein L43-A
+Macromolecule #17: 60S ribosomal protein L15-A
+Macromolecule #18: 60S ribosomal protein L11-A
+Macromolecule #19: 60S ribosomal protein L29
+Macromolecule #20: 60S ribosomal protein L17-A
+Macromolecule #21: 60S ribosomal protein L16-A
+Macromolecule #22: 60S ribosomal protein L18-A
+Macromolecule #23: 60S ribosomal protein L30
+Macromolecule #24: 60S ribosomal protein L19-A
+Macromolecule #26: 60S ribosomal protein L20-A
+Macromolecule #27: 60S ribosomal protein L31-A
+Macromolecule #28: 60S ribosomal protein L21-A
+Macromolecule #30: 60S ribosomal protein L22-A
+Macromolecule #31: 60S ribosomal protein L32
+Macromolecule #32: 60S ribosomal protein L23-A
+Macromolecule #33: 60S ribosomal protein L2-A
+Macromolecule #34: 60S ribosomal protein L24-A
+Macromolecule #35: 60S ribosomal protein L33-A
+Macromolecule #36: 60S ribosomal protein L3
+Macromolecule #37: 60S ribosomal protein L34-A
+Macromolecule #38: 60S ribosomal protein L4-A
+Macromolecule #39: 60S ribosomal protein L35-A
+Macromolecule #40: 60S ribosomal protein L5
+Macromolecule #41: 60S ribosomal protein L36-A
+Macromolecule #42: 60S ribosomal protein L6-A
+Macromolecule #43: 60S ribosomal protein L37-A
+Macromolecule #5: 25S rRNA
+Macromolecule #25: 5.8S rRNA
+Macromolecule #29: 5S rRNA
+Macromolecule #44: MAGNESIUM ION
+Macromolecule #45: CHLORIDE ION
+Macromolecule #46: SPERMIDINE
+Macromolecule #47: SPERMINE
+Macromolecule #48: ZINC ION
+Macromolecule #49: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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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: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | ![]() PDB-8p8n: |