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- PDB-9c7c: Diheteromeric GluN1/GluN2A (delM653) in nanodisc complexed with g... -

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Basic information

Entry
Database: PDB / ID: 9c7c
TitleDiheteromeric GluN1/GluN2A (delM653) in nanodisc complexed with glycine, glutamate, and GNE-4123, open conformation
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsTRANSPORT PROTEIN / ion channel / NMDA / positive allosteric modulator / open pore conformation
Function / homology
Function and homology information


regulation of response to alcohol / response to ammonium ion / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / response to environmental enrichment / directional locomotion / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / positive regulation of Schwann cell migration ...regulation of response to alcohol / response to ammonium ion / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / response to environmental enrichment / directional locomotion / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / positive regulation of Schwann cell migration / regulation of cell communication / auditory behavior / cellular response to magnesium ion / olfactory learning / response to other organism / serotonin metabolic process / response to hydrogen sulfide / dendritic branch / conditioned taste aversion / response to methylmercury / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / response to manganese ion / transmitter-gated monoatomic ion channel activity / suckling behavior / sleep / response to carbohydrate / regulation of respiratory gaseous exchange / cellular response to lipid / propylene metabolic process / response to glycine / dendritic spine organization / locomotion / cellular response to dsRNA / regulation of NMDA receptor activity / RAF/MAP kinase cascade / positive regulation of inhibitory postsynaptic potential / response to amine / neurotransmitter receptor complex / Synaptic adhesion-like molecules / response to glycoside / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / glutamate binding / voltage-gated monoatomic cation channel activity / glutamate receptor signaling pathway / ligand-gated sodium channel activity / neuromuscular process / regulation of axonogenesis / calcium ion transmembrane import into cytosol / regulation of dendrite morphogenesis / male mating behavior / protein heterotetramerization / regulation of synapse assembly / response to morphine / spinal cord development / glycine binding / dopamine metabolic process / startle response / cellular response to zinc ion / positive regulation of reactive oxygen species biosynthetic process / response to lithium ion / parallel fiber to Purkinje cell synapse / monoatomic ion channel complex / regulation of postsynaptic membrane potential / positive regulation of calcium ion transport into cytosol / associative learning / cellular response to glycine / modulation of excitatory postsynaptic potential / monoatomic cation transmembrane transport / positive regulation of dendritic spine maintenance / response to light stimulus / action potential / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of protein targeting to membrane / regulation of neuronal synaptic plasticity / monoatomic cation transport / glutamate receptor binding / social behavior / ligand-gated monoatomic ion channel activity / multicellular organismal response to stress / neuron development / conditioned place preference / prepulse inhibition / phosphatase binding / long-term memory / postsynaptic density, intracellular component / monoatomic cation channel activity / response to fungicide / synaptic cleft / calcium ion homeostasis / cellular response to manganese ion / glutamate-gated receptor activity / positive regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / cell adhesion molecule binding / neurogenesis / excitatory synapse
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Green fluorescent protein, GFP / Ionotropic glutamate receptor, metazoa / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ligated ion channel L-glutamate- and glycine-binding site ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Green fluorescent protein, GFP / Ionotropic glutamate receptor, metazoa / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
: / DECANE / DODECANE / GLUTAMIC ACID / GLYCINE / HEXANE / HEPTANE / CHOLESTEROL HEMISUCCINATE / Glutamate receptor ionotropic, NMDA 1 / Green fluorescent protein / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsJalali-Yazdi, F. / Kim, J. / Gouaux, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: Sci Adv / Year: 2025
Title: Cryo-EM snapshots of NMDA receptor activation illuminate sequential rearrangements.
Authors: Jamie A Abbott / Junhoe Kim / Beiying Liu / Gabriela K Popescu / Eric Gouaux / Farzad Jalali-Yazdi /
Abstract: Canonical -methyl-d-aspartate receptors (NMDARs) are glutamate-gated ion channels with critical roles in the development and function of the nervous system. The excitatory currents they produce ...Canonical -methyl-d-aspartate receptors (NMDARs) are glutamate-gated ion channels with critical roles in the development and function of the nervous system. The excitatory currents they produce reflect stochastic transitions between multiple agonist-bound closed- and open-pore states. We leveraged the intrinsically high open probability () of NMDARs composed of GluN1 and GluN2A subunits, together with judiciously chosen mutants and ligands, to achieve conditions in which receptors had a near unity. Using single-particle cryo-electron microscopy (cryo-EM), we captured three activated receptor states, each with distinct conformations of the gate-forming M3 helices. Separately, we carried out single-channel electrophysiology, together with statistical modeling, to relate the cryo-EM structures to the gating reaction. NMDAR channel opening involves bending of the pore-forming M3 helices to produce a transient open-channel conformation, subsequently stabilized by new interactions between the D2-M3 linkers with the pre-M1 helices and the pre-M4 loops, to yield the stable open channel.
History
DepositionJun 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Sep 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Feb 4, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1,Green fluorescent protein
B: Glutamate receptor ionotropic, NMDA 2A,Green fluorescent protein chimera
C: Glutamate receptor ionotropic, NMDA 1,Green fluorescent protein
D: Glutamate receptor ionotropic, NMDA 2A,Green fluorescent protein chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)518,21359
Polymers502,2314
Non-polymers15,98255
Water00
1


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

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Components

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Glutamate receptor ionotropic, NMDA ... , 2 types, 4 molecules ACBD

#1: Protein Glutamate receptor ionotropic, NMDA 1,Green fluorescent protein / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 124759.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Aequorea victoria (jellyfish)
Gene: Grin1, Nmdar1, GFP / Production host: Homo sapiens (human) / References: UniProt: P35439, UniProt: P42212
#2: Protein Glutamate receptor ionotropic, NMDA 2A,Green fluorescent protein chimera / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / ...GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NMDAR2A / NR2A


Mass: 126356.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Aequorea victoria (jellyfish)
Gene: Grin2a, GFP / Production host: Homo sapiens (human) / References: UniProt: Q00959, UniProt: P42212

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Sugars , 2 types, 35 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 20 molecules

#4: Chemical ChemComp-A1AUV / 4-cyclohexyl-N-[(8R)-2-cyclopropyl-7-hydroxy-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]benzene-1-sulfonamide


Mass: 427.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25N5O3S
#6: Chemical ChemComp-HP6 / HEPTANE


Mass: 100.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16
#7: Chemical
ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#9: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26
#10: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#11: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22
#12: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14

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Details

Has ligand of interestY
Has protein modificationY

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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: Diheteromeric NMDA receptor GluN1/GluN2A in nanodisc, in complex with glycine, glutamate, and GNE-4123
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.502 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Rattus norvegicus (Norway rat)10116
21Aequorea victoria (jellyfish)6100
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 9
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 53 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 8048

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
7UCSF Chimera1.16model fitting
9PHENIX1.21model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1460000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00326835
ELECTRON MICROSCOPYf_angle_d0.61836433
ELECTRON MICROSCOPYf_dihedral_angle_d8.9893925
ELECTRON MICROSCOPYf_chiral_restr0.0494224
ELECTRON MICROSCOPYf_plane_restr0.0044518

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