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Yorodumi- PDB-8tfb: Cryo-EM structure of the Methanosarcina mazei apo glutamin synthe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tfb | ||||||
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Title | Cryo-EM structure of the Methanosarcina mazei apo glutamin synthetase structure: dodecameric form | ||||||
Components | Glutamine synthetase | ||||||
Keywords | LIGASE / glutamine sythetase / GS / Methanosarcina mazei / apo / dodecamer | ||||||
Function / homology | Function and homology information polyamine catabolic process / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: M. mazei glutamine synthetase and glutamine synthetase-GlnK1 structures reveal enzyme regulation by oligomer modulation. Authors: Maria A Schumacher / Raul Salinas / Brady A Travis / Rajiv Ranjan Singh / Nicholas Lent / Abstract: Glutamine synthetases (GS) play central roles in cellular nitrogen assimilation. Although GS active-site formation requires the oligomerization of just two GS subunits, all GS form large, multi- ...Glutamine synthetases (GS) play central roles in cellular nitrogen assimilation. Although GS active-site formation requires the oligomerization of just two GS subunits, all GS form large, multi-oligomeric machines. Here we describe a structural dissection of the archaeal Methanosarcina mazei (Mm) GS and its regulation. We show that Mm GS forms unstable dodecamers. Strikingly, we show this Mm GS oligomerization property is leveraged for a unique mode of regulation whereby labile Mm GS hexamers are stabilized by binding the nitrogen regulatory protein, GlnK1. Our GS-GlnK1 structure shows that GlnK1 functions as molecular glue to affix GS hexamers together, stabilizing formation of GS active-sites. These data, therefore, reveal the structural basis for a unique form of enzyme regulation by oligomer modulation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tfb.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8tfb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8tfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tfb_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8tfb_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8tfb_validation.xml.gz | 131.6 KB | Display | |
Data in CIF | 8tfb_validation.cif.gz | 198.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/8tfb ftp://data.pdbj.org/pub/pdb/validation_reports/tf/8tfb | HTTPS FTP |
-Related structure data
Related structure data | 41228MC 8tfcC 8tfkC 8tgeC 8ufjC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 52827.926 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: glnA1, MM_0964 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PY99, glutamine synthetase #2: Chemical | ChemComp-MG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of the dodecamer form of the Methanosarcina mazei glutamine synthetase Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Methanosarcina mazei Go1 (archaea) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87200 / Symmetry type: POINT | ||||||||||||||||||||||||
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