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- EMDB-76231: Cryo EM structure of glutamine synthetase from Brucella melitensis -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-76231
TitleCryo EM structure of glutamine synthetase from Brucella melitensis
Map data
Sample
  • Complex: Dodecameric complex of glutamine synthetase
    • Protein or peptide: Glutamine synthetase, catalytic domain
KeywordsSSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / glutamine synthetase / Brucella melitensis / LIGASE
Function / homology
Function and homology information


biogenic amine catabolic process / biogenic amine metabolic process / glutamine synthetase / : / glutamine synthetase activity / ATP binding
Similarity search - Function
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, catalytic domain
Similarity search - Component
Biological speciesBrucella abortus 2308 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsLovell S / Liu L / Hammons AM / Ingham DJ / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: To be published
Title: Cryo EM structure of glutamine synthetase from Brucella melitensis
Authors: Lovell S / Liu L / Hammons AM / Ingham DJ
History
DepositionMar 20, 2026-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76231.png

Downloads & links

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Map

FileDownload / File: emd_76231.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 420 pix.
= 298.2 Å		0.71 Å/pix.
x 420 pix.
= 298.2 Å		0.71 Å/pix.
x 420 pix.
= 298.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.041
Minimum - Maximum-0.055718534 - 0.16348219
Average (Standard dev.)0.0007135313 (±0.008340876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 298.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76231_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76231_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76231_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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, catalytic domain

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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: Brucella abortus 2308 (bacteria)

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Macromolecule #1: Glutamine synthetase, catalytic domain

MacromoleculeName: Glutamine synthetase, catalytic domain / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: glutamine synthetase
Source (natural)Organism: Brucella abortus 2308 (bacteria)
Molecular weightTheoretical: 52.725621 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAHHHHHHGQ LTFDELKKAV AEGRIDTVLA CIVDMQGRLI GKRFYGQFFV ESGYDETHGC NYLLADDIDM EPVPGYEAAG WDKGYGDFV MKPDLSTLRL APWLEKTAIV LCDVLDHHHD DLSHSPRAVL KKQVQRLHER GYRAYFASEL EFYIFDETYK S ARAKRWHE ...String:
MAHHHHHHGQ LTFDELKKAV AEGRIDTVLA CIVDMQGRLI GKRFYGQFFV ESGYDETHGC NYLLADDIDM EPVPGYEAAG WDKGYGDFV MKPDLSTLRL APWLEKTAIV LCDVLDHHHD DLSHSPRAVL KKQVQRLHER GYRAYFASEL EFYIFDETYK S ARAKRWHE METASPYVQG YVIHLTTREE PVLRAMRNHL ADAGIPVENS KGEWGPGQQE LNVRYCKALE MADRHVIMKN AM KEIAEAH GKCITFMAKY DYARAGSSSH VHNSIWSADG KEPLFFDPKA PYTMTPLMRS WVAGQIKYAT DYTYFLAPYI NSY KRFQAG TFAPTKIMWS QDNRTAGFRL CGEGTKGIRI ECRIGGADIN PYLAFAALIA AGLKGVDEKL ELDEPFVGDA YSAV RLKEI PYTLREAAAA LKGSAFLKEA FGEDVVNHYT HTAHWEQIEY DRRVTDWELY RGFERY

UniProtKB: Glutamine synthetase, catalytic domain

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration2.09 mg/mL
BufferpH: 7
Details: 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide
Sugar embeddingMaterial: vitreous ice
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 1 sec. / Pretreatment - Pressure: 0.005 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 20 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

DetailsThe selected images were high-pass filtered and normalized
CTF correctionSoftware - Name: cryoSPARC (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AF-Q2YKY7-F1
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0) / Number images used: 71284
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-11zs:
Cryo EM structure of glutamine synthetase from Brucella melitensis

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