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Yorodumi- EMDB-41229: Cryo-EM structure of Methanosarcina mazie glutamine synthetase ca... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41229 | |||||||||
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Title | Cryo-EM structure of Methanosarcina mazie glutamine synthetase captured as partial oligomer | |||||||||
Map data | Mm GS apo partial oligomer | |||||||||
Sample |
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Keywords | glutamine synthetase / partial oligomer / oligomer modulation / GS regulation / LIGASE | |||||||||
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 Go1 (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.9 Å | |||||||||
Authors | Schumacher MA | |||||||||
Funding support | United States, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41229.map.gz | 31.8 MB | EMDB map data format | |
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Header (meta data) | emd-41229-v30.xml emd-41229.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
Images | emd_41229.png | 90.4 KB | ||
Filedesc metadata | emd-41229.cif.gz | 5.3 KB | ||
Others | emd_41229_half_map_1.map.gz emd_41229_half_map_2.map.gz | 62.2 MB 62.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41229 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41229 | HTTPS FTP |
-Validation report
Summary document | emd_41229_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_41229_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_41229_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | emd_41229_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41229 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41229 | HTTPS FTP |
-Related structure data
Related structure data | 8tfcMC 8tfbC 8tfkC 8tgeC 8ufjC 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_41229.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Mm GS apo partial oligomer | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Mm GS apo partial oligomer /half map A
File | emd_41229_half_map_1.map | ||||||||||||
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Annotation | Mm GS apo partial oligomer /half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Mm GS apo partial oligomer /half map B
File | emd_41229_half_map_2.map | ||||||||||||
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Annotation | Mm GS apo partial oligomer /half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : glutamine synthetase oligomer
Entire | Name: glutamine synthetase oligomer |
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Components |
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-Supramolecule #1: glutamine synthetase oligomer
Supramolecule | Name: glutamine synthetase oligomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Methanosarcina mazei Go1 (archaea) |
-Macromolecule #1: Glutamine synthetase
Macromolecule | Name: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: glutamine synthetase |
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Source (natural) | Organism: Methanosarcina mazei Go1 (archaea) |
Molecular weight | Theoretical: 52.827926 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MVQMKKCTTK EDVLEAVKER DVKFIRTQFT DTLGIIKSWA IPAEQLEEAF ENGVMFDGSS IQGFTRIEE SDMKLALDPS TFRILPWRPA TGAVARILGD VYLPDGNPFK GDPRYVLKTA IKEAEKMGFS MNVGPELEFF L FKLDANGN ...String: MGSSHHHHHH SSGLVPRGSH MVQMKKCTTK EDVLEAVKER DVKFIRTQFT DTLGIIKSWA IPAEQLEEAF ENGVMFDGSS IQGFTRIEE SDMKLALDPS TFRILPWRPA TGAVARILGD VYLPDGNPFK GDPRYVLKTA IKEAEKMGFS MNVGPELEFF L FKLDANGN PTTELTDQGG YFDFAPLDRA QDVRRDIDYA LEHMGFQIEA SHHEVAPSQH EIDFRFGDVL CTADNVVTFK YV VKSIAYH KGYYASFMPK PLFGVNGSGM HSNQSLFKDG KNVFYDPDTP TKLSQDAMYY IGGLLKHIRE FTAVTNPVVN SYK RLVPGY EAPVYISWSA QNRSSLIRIP ATRGNGTRIE LRCPDPACNP YLAFALMLRA GLEGIKNKID PGEPTNVNIF HLSD KEREE RGIRSLPADL KEAIDEMKGS KFVKEALGEH VFSHYLCAKE MEWDEYKAVV HPWELSRYLS ML UniProtKB: Glutamine synthetase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87000 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |