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- PDB-9otp: Human glutamine synthetase R298A decamer under turnover conditions -

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Basic information

Entry
Database: PDB / ID: 9otp
TitleHuman glutamine synthetase R298A decamer under turnover conditions
ComponentsGlutamine synthetase
KeywordsLIGASE / Glutamine synthetase / glutamate-ammonia ligase / Type II
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
ADENOSINE-5'-DIPHOSPHATE / Glutamine synthetase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.95 Å
AuthorsGreene, E.R. / Muniz, R.S. / Kollman, J.M. / Fraser, J.S.
Funding support United States, France, 4items
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, E.R. / Muniz, R.S. / Yamamura, H. / Hoff, S. / Bajaj, P. / Lee, D.J. / Thompson, E.M. / Arada, A. / Bonomi, M. / Kollman, J.M. / Fraser, J.S.
History
DepositionMay 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase
G: Glutamine synthetase
H: Glutamine synthetase
I: Glutamine synthetase
J: Glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,08140
Polymers420,32310
Non-polymers4,75830
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Glutamine synthetase / GS / Glutamate--ammonia ligase / Palmitoyltransferase GLUL


Mass: 42032.285 Da / Num. of mol.: 10 / Mutation: R298A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLUL, GLNS / Variant: R298A / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P15104, glutamine synthetase, protein S-acyltransferase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Glutamine synthetase R298A decamer under turnover conditions
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
160 mMHEPESC8H18N2O4S1
250 mMSodium ChlorideNaCl1
350 mMPotassium ChlorideKCl1
410 mMMagnesium ChlorideMgCl21
50.5 mMTCEPC9H15O6P1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 106000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 1.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 619435 / Symmetry type: POINT

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