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- EMDB-76061: GluA2 active state + RR2b + Glu (TMD only) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-76061
TitleGluA2 active state + RR2b + Glu (TMD only)
Map dataGluA2 active state RR2b Glu (TMD only)
Sample
  • Complex: GluA2 open state + RR2b + Glu (TMD only)
Keywordsionotropic glutamate receptor (iGluR) / iGluR / GluA2 / MEMBRANE PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.29 Å
AuthorsNewton TP / Yen LY / Gangwar SP / Sobolevsky AI
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F31NS147755 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS139087 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F31NS132554 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS083660 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS107253 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR078814 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA206573 United States
CitationJournal: Nat Commun / Year: 2026
Title: Tuning of AMPA receptor activation by inhibitory auxiliary subunits and epilepsy-associated disease mutations
Authors: Newton TP / Yelshanskaya MV / Aktolun M / Gangwar SP / Yen LY / Alekseev AA / Sobolevsky IA / Kurnikova MG / Sobolevsky AI
History
DepositionMar 13, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76061.png

Downloads & links

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Map

FileDownload / File: emd_76061.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluA2 active state RR2b Glu (TMD only)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 440 pix.
= 371.8 Å		0.85 Å/pix.
x 440 pix.
= 371.8 Å		0.85 Å/pix.
x 440 pix.
= 371.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.6445423 - 1.039879
Average (Standard dev.)0.00045955702 (±0.011674555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 371.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: GluA2 active state RR2b Glu (TMD only) half map A

Fileemd_76061_half_map_1.map
AnnotationGluA2 active state RR2b Glu (TMD only) half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GluA2 active state RR2b Glu (TMD only) half map B

Fileemd_76061_half_map_2.map
AnnotationGluA2 active state RR2b Glu (TMD only) half 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 : GluA2 open state + RR2b + Glu (TMD only)

EntireName: GluA2 open state + RR2b + Glu (TMD only)
Components
  • Complex: GluA2 open state + RR2b + Glu (TMD only)

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Supramolecule #1: GluA2 open state + RR2b + Glu (TMD only)

SupramoleculeName: GluA2 open state + RR2b + Glu (TMD only) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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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

Concentration5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris-HCl
0.05 %C56H92O29digitonin
250.0 uMC14H14N2O2(R,R)-2b
5.0 mMC5H9NO4Glutamate

Details: 150 mM NaCl, 20 mM Tris-HCl pH 8.0, and 0.05% digitonin, 250 uM (R,R)-2b, 5 mM glutamate
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 500
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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

Particle selectionNumber selected: 3623152
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: initial model from experimental data
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 245055
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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