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- EMDB-70844: Human glutamine synthetase R298A decamer under turnover conditions -

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Basic information

Entry
Database: EMDB / ID: EMD-70844
TitleHuman glutamine synthetase R298A decamer under turnover conditions
Map dataR298A variant of human glutamine synthetase under turnover conditions full
Sample
  • Complex: Glutamine synthetase R298A decamer under turnover conditions
    • Protein or peptide: Glutamine synthetase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsGlutamine synthetase / glutamate-ammonia ligase / Type II / LIGASE
Function / homology
Function and homology information


intracellular ammonium homeostasis / protein S-acyltransferase / protein palmitoylation / Astrocytic Glutamate-Glutamine Uptake And Metabolism / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamine synthetase / glutamine biosynthetic process ...intracellular ammonium homeostasis / protein S-acyltransferase / protein palmitoylation / Astrocytic Glutamate-Glutamine Uptake And Metabolism / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / Glutamate and glutamine metabolism / L-glutamate catabolic process / glial cell projection / response to glucose / positive regulation of erythrocyte differentiation / cellular response to starvation / ribosome biogenesis / cell body / angiogenesis / cell population proliferation / endoplasmic reticulum / mitochondrion / extracellular exosome / ATP binding / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / 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, 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.95 Å
AuthorsGreene ER / Muniz RS / Kollman JM / Fraser JS
Funding support United States, France, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F32GM144981-01 United States
Human Frontier Science Program (HFSP)RGP0054 France
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123159 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM145238 United States
CitationJournal: To Be Published
Title: Product-stabilized filamentation by human glutamine synthetase allosterically tunes metabolic activity
Authors: Greene ER / Muniz RS / Yamamura H / Hoff S / Bajaj P / Lee DJ / Thompson EM / Arada A / Bonomi M / Kollman JM / Fraser JS
History
DepositionMay 27, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70844.png

Downloads & links

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Map

FileDownload / File: emd_70844.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationR298A variant of human glutamine synthetase under turnover conditions full
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 256 pix.
= 169.984 Å		0.66 Å/pix.
x 256 pix.
= 169.984 Å		0.66 Å/pix.
x 256 pix.
= 169.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.664 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.15679231 - 0.3607886
Average (Standard dev.)0.0037660562 (±0.022716798)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 169.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: R298A variant of human glutamine synthetase under turnover...

Fileemd_70844_half_map_1.map
AnnotationR298A variant of human glutamine synthetase under turnover conditions half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: R298A variant of human glutamine synthetase under turnover...

Fileemd_70844_half_map_2.map
AnnotationR298A variant of human glutamine synthetase under turnover conditions half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Glutamine synthetase R298A decamer under turnover conditions

EntireName: Glutamine synthetase R298A decamer under turnover conditions
Components
  • Complex: Glutamine synthetase R298A decamer under turnover conditions
    • Protein or peptide: Glutamine synthetase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Glutamine synthetase R298A decamer under turnover conditions

SupramoleculeName: Glutamine synthetase R298A decamer under turnover conditions
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: glutamine synthetase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.032285 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTTSASSHLN KGIKQVYMSL PQGEKVQAMY IWIDGTGEGL RCKTRTLDSE PKCVEELPEW NFDGSSTLQS EGSNSDMYLV PAAMFRDPF RKDPNKLVLC EVFKYNRRPA ETNLRHTCKR IMDMVSNQHP WFGMEQEYTL MGTDGHPFGW PSNGFPGPQG P YYCGVGAD ...String:
MTTSASSHLN KGIKQVYMSL PQGEKVQAMY IWIDGTGEGL RCKTRTLDSE PKCVEELPEW NFDGSSTLQS EGSNSDMYLV PAAMFRDPF RKDPNKLVLC EVFKYNRRPA ETNLRHTCKR IMDMVSNQHP WFGMEQEYTL MGTDGHPFGW PSNGFPGPQG P YYCGVGAD RAYGRDIVEA HYRACLYAGV KIAGTNAEVM PAQWEFQIGP CEGISMGDHL WVARFILHRV CEDFGVIATF DP KPIPGNW NGAGCHTNFS TKAMREENGL KYIEEAIEKL SKRHQYHIRA YDPKGGLDNA ARLTGFHETS NINDFSAGVA NRS ASIRIP RTVGQEKKGY FEDRRPSANC DPFSVTEALI RTCLLNETGD EPFQYKN

UniProtKB: Glutamine synthetase

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 10 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 20 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.3 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
60.0 mMC8H18N2O4SHEPES
50.0 mMNaClSodium Chloride
50.0 mMKClPotassium Chloride
10.0 mMMgCl2Magnesium Chloride
0.5 mMC9H15O6PTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 106000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: OTHER
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 1.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 619435
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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