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Yorodumi- EMDB-8368: Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase L... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8368 | ||||||||||||
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Title | Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex | ||||||||||||
Map data | 60S-NMD3 complex | ||||||||||||
Sample |
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Keywords | Ribosome Biogenesis / 60S / Nmd3 / Lsg1 / Tif6 / cryo-em / RIBOSOME | ||||||||||||
Function / homology | Function and homology information 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 / ribosomal large subunit binding / 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 ...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 / ribosomal large subunit binding / 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 / translational elongation / carbohydrate transmembrane transporter activity / maltose binding / ribosomal large subunit export from nucleus / maltose transport / maltodextrin transmembrane transport / protein-RNA complex assembly / regulation of translational fidelity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / translational termination / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / translational initiation / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / protein transport / ribosome biogenesis / protein-macromolecule adaptor activity / 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 / nucleolus / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||
Authors | Malyutin AG / Musalgaonkar S / Patchett S / Frank J / Johnson AW | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: EMBO J / Year: 2017 Title: Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis. Authors: Andrey G Malyutin / Sharmishtha Musalgaonkar / Stephanie Patchett / Joachim Frank / Arlen W Johnson / Abstract: During ribosome biogenesis in eukaryotes, nascent subunits are exported to the cytoplasm in a functionally inactive state. 60S subunits are activated through a series of cytoplasmic maturation events. ...During ribosome biogenesis in eukaryotes, nascent subunits are exported to the cytoplasm in a functionally inactive state. 60S subunits are activated through a series of cytoplasmic maturation events. The last known events in the cytoplasm are the release of Tif6 by Efl1 and Sdo1 and the release of the export adapter, Nmd3, by the GTPase Lsg1. Here, we have used cryo-electron microscopy to determine the structure of the 60S subunit bound by Nmd3, Lsg1, and Tif6. We find that a central domain of Nmd3 mimics the translation elongation factor eIF5A, inserting into the E site of the ribosome and pulling the L1 stalk into a closed position. Additional domains occupy the P site and extend toward the sarcin-ricin loop to interact with Tif6. Nmd3 and Lsg1 together embrace helix 69 of the B2a intersubunit bridge, inducing base flipping that we suggest may activate the GTPase activity of Lsg1. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8368.map.gz | 14.6 MB | EMDB map data format | |
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Header (meta data) | emd-8368-v30.xml emd-8368.xml | 70.8 KB 70.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8368_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_8368.png | 182.9 KB | ||
Filedesc metadata | emd-8368.cif.gz | 14.1 KB | ||
Others | emd_8368_half_map_1.map.gz emd_8368_half_map_2.map.gz | 98.5 MB 98.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8368 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8368 | HTTPS FTP |
-Validation report
Summary document | emd_8368_validation.pdf.gz | 972.8 KB | Display | EMDB validaton report |
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Full document | emd_8368_full_validation.pdf.gz | 972.4 KB | Display | |
Data in XML | emd_8368_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | emd_8368_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8368 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8368 | HTTPS FTP |
-Related structure data
Related structure data | 5t6rMC 8362C 5t62C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8368.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 60S-NMD3 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: 60S-NMD3 complex half map 1
File | emd_8368_half_map_1.map | ||||||||||||
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Annotation | 60S-NMD3 complex half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 60S-NMD3 complex half map 2
File | emd_8368_half_map_2.map | ||||||||||||
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Annotation | 60S-NMD3 complex half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 60S in complex with Nmd3
+Supramolecule #1: 60S in complex with Nmd3
+Macromolecule #1: 25S Ribosomal RNA
+Macromolecule #2: 5S Ribosomal RNA
+Macromolecule #3: 5.8S Ribosomal RNA
+Macromolecule #4: 60S ribosomal protein L2-A
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4-A
+Macromolecule #7: 60S ribosomal protein L5
+Macromolecule #8: 60S ribosomal protein L6-A
+Macromolecule #9: 60S ribosomal protein L7-A
+Macromolecule #10: 60S ribosomal protein L8-A
+Macromolecule #11: 60S ribosomal protein L9-A
+Macromolecule #12: 60S ribosomal protein L10
+Macromolecule #13: 60S ribosomal protein L11-A
+Macromolecule #14: 60S ribosomal protein L13-A
+Macromolecule #15: 60S ribosomal protein L14-A
+Macromolecule #16: 60S ribosomal protein L15-A
+Macromolecule #17: 60S ribosomal protein L16-A
+Macromolecule #18: 60S ribosomal protein L17-A
+Macromolecule #19: 60S ribosomal protein L18-A
+Macromolecule #20: 60S ribosomal protein L19-A
+Macromolecule #21: 60S ribosomal protein L20-A
+Macromolecule #22: 60S ribosomal protein L21-A
+Macromolecule #23: 60S ribosomal protein L22-A
+Macromolecule #24: 60S ribosomal protein L23-A
+Macromolecule #25: 60S ribosomal protein L24-A
+Macromolecule #26: 60S ribosomal protein L25
+Macromolecule #27: 60S ribosomal protein L26-A
+Macromolecule #28: 60S ribosomal protein L27-A
+Macromolecule #29: 60S ribosomal protein L28
+Macromolecule #30: 60S ribosomal protein L29
+Macromolecule #31: 60S ribosomal protein L30
+Macromolecule #32: 60S ribosomal protein L31-A
+Macromolecule #33: 60S ribosomal protein L32
+Macromolecule #34: 60S ribosomal protein L33-A
+Macromolecule #35: 60S ribosomal protein L34-A
+Macromolecule #36: 60S ribosomal protein L35-A
+Macromolecule #37: 60S ribosomal protein L36-A
+Macromolecule #38: 60S ribosomal protein L37-A
+Macromolecule #39: 60S ribosomal protein L38
+Macromolecule #40: 60S ribosomal protein L39
+Macromolecule #41: Ubiquitin-60S ribosomal protein L40
+Macromolecule #42: 60S ribosomal protein L42-A
+Macromolecule #43: 60S ribosomal protein L43-A
+Macromolecule #44: Ribosomal Protein uL1
+Macromolecule #45: Maltose binding protein, 60S ribosomal export protein Nmd3 fusion
+Macromolecule #46: MAGNESIUM ION
+Macromolecule #47: POTASSIUM ION
+Macromolecule #48: water
-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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Grid | Model: Made in lab / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER / Details: 10W |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Average exposure time: 8.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 30.0 µm / Calibrated magnification: 31000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 27000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | PDB-5t6r: |