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Yorodumi- PDB-5t62: Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t62 | ||||||||||||
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Title | Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex | ||||||||||||
Components |
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Keywords | RIBOSOME / Ribosome Biogenesis / 60S / Nmd3 / Lsg1 / Tif6 / cryo-em | ||||||||||||
Function / homology | Function and homology information mating projection tip / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / maturation of 5.8S rRNA / 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 ...mating projection tip / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / maturation of 5.8S rRNA / 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 / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / ribosomal subunit export from nucleus / translational termination / translation initiation factor activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / 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 / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Saccharomyces cerevisiae S288c (yeast) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Malyutin, A.G. / Musalgaonkar, S. / Patchett, S. / Frank, J. / Johnson, A.W. | ||||||||||||
Funding support | United States, 3items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5t62.cif.gz | 3.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5t62.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5t62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t62_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5t62_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5t62_validation.xml.gz | 211.4 KB | Display | |
Data in CIF | 5t62_validation.cif.gz | 373.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/5t62 ftp://data.pdbj.org/pub/pdb/validation_reports/t6/5t62 | HTTPS FTP |
-Related structure data
Related structure data | 8362MC 8368C 5t6rC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 5 molecules XzSVW
#1: Protein | Mass: 28597.959 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: TIF6, CDC95, YPR016C, LPZ15C / Plasmid: pAJ3283 / Details (production host): 6HIS-kemptide-TIF6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12522 |
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#42: Protein | Mass: 14583.077 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P0CH08 |
#45: Protein | Mass: 18485.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
#46: Protein | Mass: 59995.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P38861 |
#47: Protein | Mass: 71945.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c References: UniProt: P53145, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
-RNA chain , 3 types, 3 molecules ABC
#2: RNA chain | Mass: 1097493.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: REF: 831416132 |
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#3: RNA chain | Mass: 38951.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039024045 |
#4: RNA chain | Mass: 50682.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1102645687 |
+60S ribosomal protein ... , 39 types, 39 molecules DEFGHIJKLMNOabcdefghijklmnopqr...
-Non-polymers , 4 types, 169 molecules
#48: Chemical | ChemComp-MG / #49: Chemical | #50: Chemical | ChemComp-GNP / | #51: Water | ChemComp-HOH / | |
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-Details
Sequence details | In chain 47 the two UNK segments (135-175 and 276-298) are separated by gaps from the rest of the ...In chain 47 the two UNK segments (135-175 and 276-298) are separated by gaps from the rest of the known sequence and there is not enough information in my EM maps to accurately assign neither the number nor sequence to these regions |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Specimen support |
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Vitrification |
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-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company / Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||||||||||||||||||||
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EM imaging | Accelerating voltage: 300 kV / Cryogen: NITROGEN / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELD / Specimen-ID: 1
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Image recording |
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-Processing
Software | Name: REFMAC / Version: 5.8.0088 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Image processing |
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CTF correction |
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Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction |
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Atomic model building | Protocol: OTHER | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 131777 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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