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- EMDB-48914: CryoEM structure of the Azotobacter vinelandii glutamine synthetase -

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Basic information

Entry
Database: EMDB / ID: EMD-48914
TitleCryoEM structure of the Azotobacter vinelandii glutamine synthetase
Map data
Sample
  • Complex: Dodecameric complex of glutamine synthetase
    • Protein or peptide: Glutamine synthetase
Keywordsnitrogen metabolism / LIGASE
Function / homology
Function and homology information


nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / nitrogen fixation / ATP binding / metal ion binding / membrane / cytoplasm
Similarity search - Function
Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily ...Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Glutamine synthetase
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWarmack RA / Shen Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143836 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM152765 United States
CitationJournal: Structure / Year: 2025
Title: CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes.
Authors: Yuanbo Shen / Ailiena O Maggiolo / Tianzheng Zhang / Rebeccah A Warmack /
Abstract: Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry ...Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry and machine learning, they promise to facilitate the visual exploration of proteomes. Leveraging visual proteomics, we interrogate structures isolated from a complex cellular milieu by cryoEM to identify and classify molecular structures and complexes de novo. By comparing three automated model building programs, CryoID, DeepTracer, and ModelAngelo, we determine the identity of six distinct oligomeric protein complexes from partially purified extracts of the nitrogen-fixing bacterium Azotobacter vinelandii using both anaerobic and aerobic cryoEM, including two original oligomeric structures. Overall, by allowing the study of near-native oligomeric protein states, cryoEM-enabled visual proteomics reveals unique structures that correspond to relevant species observed in situ.
History
DepositionFeb 3, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48914.png

Downloads & links

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Map

FileDownload / File: emd_48914.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 576 pix.
= 374.4 Å		0.65 Å/pix.
x 576 pix.
= 374.4 Å		0.65 Å/pix.
x 576 pix.
= 374.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.42952502 - 0.7748202
Average (Standard dev.)0.00036856512 (±0.03287566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 374.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48914_half_map_1.map
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Half map: #1

Fileemd_48914_half_map_2.map
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Sample components

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Entire : Dodecameric complex of glutamine synthetase

EntireName: Dodecameric complex of glutamine synthetase
Components
  • Complex: Dodecameric complex of glutamine synthetase
    • Protein or peptide: Glutamine synthetase

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Supramolecule #1: Dodecameric complex of glutamine synthetase

SupramoleculeName: Dodecameric complex of glutamine synthetase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ

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Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: glutamine synthetase
Source (natural)Organism: Azotobacter vinelandii (bacteria) / Strain: DJ
Molecular weightTheoretical: 51.809254 KDa
SequenceString: MSKSLQLIKE HDVKWIDLRF TDTKGKQQHV TMPARDVDDD FFEYGKMFDG SSIAGWKGIE ASDMILMPDD STAVLDPFTE EPTLIIVCD IIEPSTMQGY DRDPRAIARR AEEYLKSTGI GDTAFFGPEP EFFIFDEVKY KSDISGSMFK IFSEQAAWNT D ADFEGGNK ...String:
MSKSLQLIKE HDVKWIDLRF TDTKGKQQHV TMPARDVDDD FFEYGKMFDG SSIAGWKGIE ASDMILMPDD STAVLDPFTE EPTLIIVCD IIEPSTMQGY DRDPRAIARR AEEYLKSTGI GDTAFFGPEP EFFIFDEVKY KSDISGSMFK IFSEQAAWNT D ADFEGGNK GHRPGVKGGY FPVPPVDHDH EIRTAMCNAL EEMGLKVEVH HHEVATAGQN EIGVSFNTLV AKADEVQTLK YC VHNVADA YGKTVTFMPK PLYGDNGSGM HVHMSIAKDG KNTFAGEGYA GLSDTALYFI GGIIKHGKAL NGFTNPSTNS YKR LVPGFE APVMLAYSAR NRSASIRIPY VNSPKARRIE ARFPDPSANP YLAFAALLMA GLDGIQNKIH PGDAADKNLY DLPP EEAKE IPQVCGSLKE ALEELDKGRA FLTKGGVFSD DFIDAYLELK SEEEIKVRTF VHPLEYDLYY SV

UniProtKB: Glutamine synthetase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -3.0 µm / Nominal defocus min: -0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 10672
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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