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- EMDB-38450: Structure of the native glutamine synthetase in the adult cortex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-38450
TitleStructure of the native glutamine synthetase in the adult cortex and hippocampus
Map data
Sample
  • Complex: Decamer of Glutamine synthetase from rat brain
    • Protein or peptide: Glutamine synthetase
KeywordsNative glutamine synthetase / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


Astrocytic Glutamate-Glutamine Uptake And Metabolism / Glutamate and glutamine metabolism / intracellular ammonium homeostasis / ammonia assimilation cycle / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration ...Astrocytic Glutamate-Glutamine Uptake And Metabolism / Glutamate and glutamine metabolism / intracellular ammonium homeostasis / ammonia assimilation cycle / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of protein localization to nucleolus / regulation of sprouting angiogenesis / regulation of endothelial cell migration / dynein light chain binding / glutamate metabolic process / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / glutamate binding / nickel cation binding / glial cell projection / positive regulation of synaptic transmission, glutamatergic / response to glucose / axon terminus / positive regulation of erythrocyte differentiation / cellular response to starvation / positive regulation of epithelial cell proliferation / cell projection / positive regulation of insulin secretion / ribosome biogenesis / myelin sheath / manganese ion binding / cell body / angiogenesis / perikaryon / cell population proliferation / magnesium ion binding / endoplasmic reticulum / protein-containing complex / mitochondrion / ATP binding / identical protein binding / 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 speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsZhang M / Feng J / Li Y / Zhu S
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Cell / Year: 2025
Title: Assembly and architecture of endogenous NMDA receptors in adult cerebral cortex and hippocampus.
Authors: Ming Zhang / Juan Feng / Chun Xie / Nan Song / Chaozhi Jin / Jian Wang / Qun Zhao / Lihua Zhang / Boshuang Wang / Yidi Sun / Fei Guo / Yang Li / Shujia Zhu /
Abstract: The cerebral cortex and hippocampus are crucial brain regions for learning and memory, which depend on activity-induced synaptic plasticity involving N-methyl-ᴅ-aspartate receptors (NMDARs). ...The cerebral cortex and hippocampus are crucial brain regions for learning and memory, which depend on activity-induced synaptic plasticity involving N-methyl-ᴅ-aspartate receptors (NMDARs). However, subunit assembly and molecular architecture of endogenous NMDARs (eNMDARs) in the brain remain elusive. Using conformation- and subunit-dependent antibodies, we purified eNMDARs from adult rat cerebral cortex and hippocampus. Three major subtypes of GluN1-N2A-N2B, GluN1-N2B, and GluN1-N2A eNMDARs were resolved by cryoelectron microscopy (cryo-EM) at the resolution up to 4.2 Å. The particle ratio of these three subtypes was 9:7:4, indicating that about half of GluN2A and GluN2B subunits are incorporated into the tri-heterotetramers. Structural analysis revealed the asymmetric architecture of the GluN1-N2A-N2B receptor throughout the extracellular to the transmembrane layers. Moreover, the conformational variations between GluN1-N2B and GluN1-N2A-N2B receptors revealed the distinct biophysical properties across different eNMDAR subtypes. Our findings imply the structural and functional complexity of eNMDARs and shed light on structure-based therapeutic design targeting these eNMDARs in vivo.
History
DepositionDec 26, 2023-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38450.png

Downloads & links

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Map

FileDownload / File: emd_38450.map.gz / Format: CCP4 / Size: 303.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 430 pix.
= 460.53 Å		1.07 Å/pix.
x 430 pix.
= 460.53 Å		1.07 Å/pix.
x 430 pix.
= 460.53 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.95172393 - 1.1764706
Average (Standard dev.)0.00016981702 (±0.023153722)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions430430430
Spacing430430430
CellA=B=C: 460.53 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38450_msk_1.map
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Half map: #1

Fileemd_38450_half_map_1.map
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Half map: #2

Fileemd_38450_half_map_2.map
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Sample components

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Entire : Decamer of Glutamine synthetase from rat brain

EntireName: Decamer of Glutamine synthetase from rat brain
Components
  • Complex: Decamer of Glutamine synthetase from rat brain
    • Protein or peptide: Glutamine synthetase

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Supramolecule #1: Decamer of Glutamine synthetase from rat brain

SupramoleculeName: Decamer of Glutamine synthetase from rat brain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 600 MDa

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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: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 42.209672 KDa
SequenceString: MATSASSHLN KGIKQMYMNL PQGEKIQLMY IWVDGTGEGL RCKTRTLDCD PKCVEELPEW NFDGSSTFQS EGSNSDMYLH PVAMFRDPF RRDPNKLVFC EVFKYNRKPA ETNLRHSCKR IMDMVSSQHP WFGMEQEYTL MGTDGHPFGW PSNGFPGPQG P YYCGVGAD ...String:
MATSASSHLN KGIKQMYMNL PQGEKIQLMY IWVDGTGEGL RCKTRTLDCD PKCVEELPEW NFDGSSTFQS EGSNSDMYLH PVAMFRDPF RRDPNKLVFC EVFKYNRKPA ETNLRHSCKR IMDMVSSQHP WFGMEQEYTL MGTDGHPFGW PSNGFPGPQG P YYCGVGAD KAYGRDIVEA HYRACLYAGI KITGTNAEVM PAQWEFQIGP CEGIRMGDHL WVARFILHRV CEDFGVIATF DP KPIPGNW NGAGCHTNFS TKAMREENGL RCIEEAIDKL SKRHQYHIRA YDPKGGLDNA RRLTGFHETS NINDFSAGVA NRS ASIRIP RIVGQEKKGY FEDRRPSANC DPYAVTEAIV RTCLLNETGD EPFQYK

UniProtKB: Glutamine synthetase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE
Detailsrat brain Glutamine synthetase

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-10 (5k 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: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159453
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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