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Yorodumi- EMDB-32352: Structural of the filamentous Escherichia coli glutamine synthetase -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32352 | |||||||||
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Title | Structural of the filamentous Escherichia coli glutamine synthetase | |||||||||
Map data | SPA map of Ecoli GS filament, calculated using cryoSPARC. | |||||||||
Sample |
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Function / homology | Function and homology information ammonia assimilation cycle / nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / response to radiation / ATP binding / membrane / identical protein binding / metal ion binding ...ammonia assimilation cycle / nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / response to radiation / ATP binding / membrane / identical protein binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli BL21(DE3) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.94 Å | |||||||||
Authors | Huang P-C / Chen S-K / Wu K-P | |||||||||
Funding support | Taiwan, 2 items
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Citation | Journal: Protein Sci / Year: 2022 Title: Structural basis for the helical filament formation of Escherichia coli glutamine synthetase. Authors: Pei-Chi Huang / Shao-Kang Chen / Wei-Hung Chiang / Meng-Ru Ho / Kuen-Phon Wu / Abstract: Escherichia coli glutamine synthetase (EcGS) spontaneously forms a dodecamer that catalytically converts glutamate to glutamine. EcGS stacks with other dodecamers to create a filament-like polymer ...Escherichia coli glutamine synthetase (EcGS) spontaneously forms a dodecamer that catalytically converts glutamate to glutamine. EcGS stacks with other dodecamers to create a filament-like polymer visible under transmission electron microscopy. Filamentous EcGS is induced by environmental metal ions. We used cryo-electron microscopy (cryo-EM) to decipher the structure of metal ion (nickel)-induced EcGS helical filament at a sub-3Å resolution. EcGS filament formation involves stacking of native dodecamers by chelating nickel ions to residues His5 and His13 in the first N-terminal helix (H1). His5 and His13 from paired parallel H1 helices provide salt bridges and hydrogen bonds to tightly stack two dodecamers. One subunit of the EcGS filament hosts two nickel ions, whereas the dodecameric interface and the ATP/Mg-binding site both host a nickel ion each. We reveal that upon adding glutamate or ATP for catalytic reactions, nickel-induced EcGS filament reverts to individual dodecamers. Such tunable filament formation is often associated with stress responses. Our results provide detailed structural information on the mechanism underlying reversible and tunable EcGS filament formation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32352.map.gz | 286.1 MB | EMDB map data format | |
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Header (meta data) | emd-32352-v30.xml emd-32352.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
Images | emd_32352.png | 97 KB | ||
Others | emd_32352_additional_1.map.gz emd_32352_additional_2.map.gz | 230 MB 277.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32352 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32352 | HTTPS FTP |
-Related structure data
Related structure data | 7w85MC 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_32352.map.gz / Format: CCP4 / Size: 303.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | SPA map of Ecoli GS filament, calculated using cryoSPARC. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Helical reconstruction map of Ecoli GS filament, calculated...
File | emd_32352_additional_1.map | ||||||||||||
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Annotation | Helical reconstruction map of Ecoli GS filament, calculated using cryoSPARC. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: additional map for the 24mer (12mer x2) assembly....
File | emd_32352_additional_2.map | ||||||||||||
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Annotation | additional map for the 24mer (12mer x2) assembly. It was calculated to 5.5 angstrom. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Filamentous form of Ecoli glutamine synthetase
Entire | Name: Filamentous form of Ecoli glutamine synthetase |
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Components |
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-Supramolecule #1: Filamentous form of Ecoli glutamine synthetase
Supramolecule | Name: Filamentous form of Ecoli glutamine synthetase / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #1: Glutamine synthetase
Macromolecule | Name: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: glutamine synthetase |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 51.966609 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSAEHVLTML NEHEVKFVDL RFTDTKGKEQ HVTIPAHQVN AEFFEEGKMF DGSSIGGWKG INESDMVLMP DASTAVIDPF FADSTLIIR CDILEPGTLQ GYDRDPRSIA KRAEDYLRST GIADTVLFGP EPEFFLFDDI RFGSSISGSH VAIDDIEGAW N SSTQYEGG ...String: MSAEHVLTML NEHEVKFVDL RFTDTKGKEQ HVTIPAHQVN AEFFEEGKMF DGSSIGGWKG INESDMVLMP DASTAVIDPF FADSTLIIR CDILEPGTLQ GYDRDPRSIA KRAEDYLRST GIADTVLFGP EPEFFLFDDI RFGSSISGSH VAIDDIEGAW N SSTQYEGG NKGHRPAVKG GYFPVPPVDS AQDIRSEMCL VMEQMGLVVE AHHHEVATAG QNEVATRFNT MTKKADEIQI YK YVVHNVA HRFGKTATFM PKPMFGDNGS GMHCHMSLSK NGVNLFAGDK YAGLSEQALY YIGGVIKHAK AINALANPTT NSY KRLVPG YEAPVMLAYS ARNRSASIRI PVVSSPKARR IEVRFPDPAA NPYLCFAALL MAGLDGIKNK IHPGEAMDKN LYDL PPEEA KEIPQVAGSL EEALNELDLD REFLKAGGVF TDEAIDAYIA LRREEDDRVR MTPHPVEFEL YYSV |
-Macromolecule #2: NICKEL (II) ION
Macromolecule | Name: NICKEL (II) ION / type: ligand / ID: 2 / Number of copies: 42 / Formula: NI |
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Molecular weight | Theoretical: 58.693 Da |
Chemical component information | ChemComp-NI: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
Details | Titan Krios |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1182 / Average electron dose: 59.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software: (Name: cryoSPARC (ver. 2.14), cryoSPARC (ver. 3.2)) |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2) |
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 117242 |