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- EMDB-70404: GluN1/GluN3A_ELSL in complex with CGP/GLY/GNE/UCM, LBD-TMD focuse... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-70404
TitleGluN1/GluN3A_ELSL in complex with CGP/GLY/GNE/UCM, LBD-TMD focused, in active state (class 3)
Map dataGluN1/GluN3A_ELSL in complex with CGP/GLY/GNE/UCM, LBD-TMD focused, in active state (class 3)
Sample
  • Complex: Di-heteromeric GluN1/GluN3A_ELSL NMDA receptor in complex with CGP/Gly/GNE/UCM, LBD-TMD focused, in active conformation (class 3)
Keywordsligand-gated ion channel / agonist / antagonist / complex / TRANSPORT PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.06 Å
AuthorsKim J / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: To Be Published
Title: GluN1/GluN3A_ELSL in complex with CGP/GLY/GNE/UCM, LBD-TMD focused, in active state (class 3)
Authors: Kim J / Gouaux E
History
DepositionApr 29, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70404.png

Downloads & links

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Map

FileDownload / File: emd_70404.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluN1/GluN3A_ELSL in complex with CGP/GLY/GNE/UCM, LBD-TMD focused, in active state (class 3)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 512 pix.
= 380.416 Å		0.74 Å/pix.
x 512 pix.
= 380.416 Å		0.74 Å/pix.
x 512 pix.
= 380.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.058
Minimum - Maximum-0.11344354 - 0.25251913
Average (Standard dev.)0.00087906263 (±0.00814636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 380.416 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_70404_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_70404_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Di-heteromeric GluN1/GluN3A_ELSL NMDA receptor in complex with CG...

EntireName: Di-heteromeric GluN1/GluN3A_ELSL NMDA receptor in complex with CGP/Gly/GNE/UCM, LBD-TMD focused, in active conformation (class 3)
Components
  • Complex: Di-heteromeric GluN1/GluN3A_ELSL NMDA receptor in complex with CGP/Gly/GNE/UCM, LBD-TMD focused, in active conformation (class 3)

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Supramolecule #1: Di-heteromeric GluN1/GluN3A_ELSL NMDA receptor in complex with CG...

SupramoleculeName: Di-heteromeric GluN1/GluN3A_ELSL NMDA receptor in complex with CGP/Gly/GNE/UCM, LBD-TMD focused, in active conformation (class 3)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 411 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

Concentration4 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 290 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 7622 / Average electron dose: 50.0 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
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model from 2D class average
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 14421
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

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