+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25863 | ||||||||||||
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Title | S. aureus GS(12)-Q-GlnR peptide | ||||||||||||
Map data | Sharpened (B factor 62A^2) | ||||||||||||
Sample |
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Keywords | glutamine synthetase repressor dodecamer / BIOSYNTHETIC PROTEIN / LIGASE | ||||||||||||
Function / homology | Function and homology information glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / DNA-binding transcription factor activity / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.15 Å | ||||||||||||
Authors | Travis BA / Peck J | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria. Authors: Brady A Travis / Jared V Peck / Raul Salinas / Brandon Dopkins / Nicholas Lent / Viet D Nguyen / Mario J Borgnia / Richard G Brennan / Maria A Schumacher / Abstract: How bacteria sense and respond to nitrogen levels are central questions in microbial physiology. In Gram-positive bacteria, nitrogen homeostasis is controlled by an operon encoding glutamine ...How bacteria sense and respond to nitrogen levels are central questions in microbial physiology. In Gram-positive bacteria, nitrogen homeostasis is controlled by an operon encoding glutamine synthetase (GS), a dodecameric machine that assimilates ammonium into glutamine, and the GlnR repressor. GlnR detects nitrogen excess indirectly by binding glutamine-feedback-inhibited-GS (FBI-GS), which activates its transcription-repression function. The molecular mechanisms behind this regulatory circuitry, however, are unknown. Here we describe biochemical and structural analyses of GS and FBI-GS-GlnR complexes from pathogenic and non-pathogenic Gram-positive bacteria. The structures show FBI-GS binds the GlnR C-terminal domain within its active-site cavity, juxtaposing two GlnR monomers to form a DNA-binding-competent GlnR dimer. The FBI-GS-GlnR interaction stabilizes the inactive GS conformation. Strikingly, this interaction also favors a remarkable dodecamer to tetradecamer transition in some GS, breaking the paradigm that all bacterial GS are dodecamers. These data thus unveil unique structural mechanisms of transcription and enzymatic regulation. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25863.map.gz | 230.3 MB | EMDB map data format | |
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Header (meta data) | emd-25863-v30.xml emd-25863.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_25863.png | 119.9 KB | ||
Filedesc metadata | emd-25863.cif.gz | 5.7 KB | ||
Others | emd_25863_additional_1.map.gz | 123.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25863 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25863 | HTTPS FTP |
-Validation report
Summary document | emd_25863_validation.pdf.gz | 598 KB | Display | EMDB validaton report |
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Full document | emd_25863_full_validation.pdf.gz | 597.6 KB | Display | |
Data in XML | emd_25863_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_25863_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25863 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25863 | HTTPS FTP |
-Related structure data
Related structure data | 7tf6MC 7tdpC 7tdvC 7teaC 7tecC 7tenC 7tf7C 7tf9C 7tfaC 7tfbC 7tfcC 7tfdC 7tfeC 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_25863.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened (B factor 62A^2) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_25863_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dodecameric GS complex with glutamine and GlnR C-tail peptides
Entire | Name: Dodecameric GS complex with glutamine and GlnR C-tail peptides |
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Components |
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-Supramolecule #1: Dodecameric GS complex with glutamine and GlnR C-tail peptides
Supramolecule | Name: Dodecameric GS complex with glutamine and GlnR C-tail peptides type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Macromolecule #1: Glutamine synthetase
Macromolecule | Name: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: glutamine synthetase |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Molecular weight | Theoretical: 51.19684 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSHMPKRTFT KEDIRKFAEE ENVRYLRLQF TDILGTIKNV EVPVSQLEKV LDNEMMFDGS SIEGFVRIEE SDMYLHPDLD TWVIFPWTA GQGKVARLIC DVYKTDGTPF EGDPRANLKR VLKEMEDLGF TDFNLGPEPE FFLFKLDEKG EPTLELNDDG G YFDLAPTD ...String: GSHMPKRTFT KEDIRKFAEE ENVRYLRLQF TDILGTIKNV EVPVSQLEKV LDNEMMFDGS SIEGFVRIEE SDMYLHPDLD TWVIFPWTA GQGKVARLIC DVYKTDGTPF EGDPRANLKR VLKEMEDLGF TDFNLGPEPE FFLFKLDEKG EPTLELNDDG G YFDLAPTD LGENCRRDIV LELEDMGFDI EASHHEVAPG QHEIDFKYAD AVTACDNIQT FKLVVKTIAR KHNLHATFMP KP LFGVNGS GMHFNVSLFK GKENAFFDPN TEMGLTETAY QFTAGVLKNA RGFTAVCNPL VNSYKRLVPG YEAPCYIAWS GKN RSPLIR VPSSRGLSTR IEVRSVDPAA NPYMALAAIL EAGLDGIKNK LKVPEPVNQN IYEMNREERE AVGIQDLPST LYTA LKAMR ENEVIKKALG NHIYNQFINS KSIEWDYYRT QVSEWERDQY MKQY UniProtKB: Glutamine synthetase |
-Macromolecule #2: Peptide from Glutamine synthetase repressor
Macromolecule | Name: Peptide from Glutamine synthetase repressor / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
Molecular weight | Theoretical: 1.289485 KDa |
Sequence | String: PINRGDLSRF I UniProtKB: Glutamine synthetase repressor |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 24 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: GLUTAMINE
Macromolecule | Name: GLUTAMINE / type: ligand / ID: 4 / Number of copies: 12 / Formula: GLN |
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Molecular weight | Theoretical: 146.144 Da |
Chemical component information | ChemComp-GLN: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.75 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.5 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 222918 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2) |
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-7tf6: |