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- EMDB-46520: TMD local refined map of Gly-,Glu-,(S)-DQP-997-74 bound NMDAR -

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Basic information

Entry
Database: EMDB / ID: EMD-46520
TitleTMD local refined map of Gly-,Glu-,(S)-DQP-997-74 bound NMDAR
Map dataTMD local refined map of Gly-,Glu-,(S)-DQP-997-74 bound NMDAR
Sample
  • Complex: tri-heteromeric GluN1-2B-2D NMDAR
KeywordsN-methyl-D-aspartate receptor / (S)-DQP-997-74 / GluN2B / GluN2D / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.07 Å
AuthorsHyunook K / Hiro F
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS111745 United States
CitationJournal: Neuron / Year: 2025
Title: Structural basis for channel gating and blockade in tri-heteromeric GluN1-2B-2D NMDA receptor.
Authors: Hyunook Kang / Max Epstein / Tue G Banke / Riley Perszyk / Noriko Simorowski / Srinu Paladugu / Dennis C Liotta / Stephen F Traynelis / Hiro Furukawa /
Abstract: Discrete activation of N-methyl-D-aspartate receptor (NMDAR) subtypes by glutamate and the co-agonist glycine is fundamental to neuroplasticity. A distinct variant, the tri-heteromeric receptor, ...Discrete activation of N-methyl-D-aspartate receptor (NMDAR) subtypes by glutamate and the co-agonist glycine is fundamental to neuroplasticity. A distinct variant, the tri-heteromeric receptor, comprising glycine-binding GluN1 and two types of glutamate-binding GluN2 subunits, exhibits unique pharmacological characteristics, notably enhanced sensitivity to the anti-depressant channel blocker S-(+)-ketamine. Despite its significance, the structural mechanisms underlying ligand gating and channel blockade of tri-heteromeric NMDARs remain poorly understood. Here, we identify and characterize tri-heteromeric GluN1-2B-2D NMDAR in the adult brain, resolving its structures in the activated, inhibited, and S-(+)-ketamine-blocked states. These structures reveal the ligand-dependent conformational dynamics that modulate the tension between the extracellular domain and transmembrane channels, governing channel gating and blockade. Additionally, we demonstrate that the inhibitor (S)-DQP-997-74 selectively decouples linker tension in GluN2D, offering insights into subtype-selective targeting for cognitive modulation.
History
DepositionAug 9, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46520.png

Downloads & links

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Map

FileDownload / File: emd_46520.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTMD local refined map of Gly-,Glu-,(S)-DQP-997-74 bound NMDAR
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 344.4 Å		0.86 Å/pix.
x 400 pix.
= 344.4 Å		0.86 Å/pix.
x 400 pix.
= 344.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.861 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.4777856 - 1.9084847
Average (Standard dev.)0.0015326604 (±0.032218512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_46520_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_46520_half_map_2.map
AnnotationHalf 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 : tri-heteromeric GluN1-2B-2D NMDAR

EntireName: tri-heteromeric GluN1-2B-2D NMDAR
Components
  • Complex: tri-heteromeric GluN1-2B-2D NMDAR

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Supramolecule #1: tri-heteromeric GluN1-2B-2D NMDAR

SupramoleculeName: tri-heteromeric GluN1-2B-2D NMDAR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 377 KDa

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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

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 14 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1317548
CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: OTHER / Details: Ab initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 100870
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7saa

chain_id: A, source_name: PDB, initial_model_type: experimental model

7saa

chain_id: B, source_name: PDB, initial_model_type: experimental model

7saa

chain_id: C, source_name: PDB, initial_model_type: experimental model

8e96

chain_id: D, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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