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- EMDB-76105: GluA2-STZ pre-active state with partial agonist kainic acid (KA) ... -

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Basic information

Entry
Database: EMDB / ID: EMD-76105
TitleGluA2-STZ pre-active state with partial agonist kainic acid (KA) at 25 degrees C (ATD only)
Map dataATD
Sample
  • Complex: GluA2-STZ pre-active state with partial agonist kainic acid (KA) at 25 degrees C (ATD only)
Keywordsionotropic glutamate receptor (iGluR) / iGluR / GluA2 / transmembrane AMPAR regulatory protein (TARP) y2 / gamma2 / stargazin (STZ) / MEMBRANE PROTEIN
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.98 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 Struct Mol Biol / Year: 2026
Title: Pre-activation and gating pathway of AMPA receptors revealed by full and partial agonists.
Authors: Thomas P Newton / Muhammed Aktolun / Maria V Yelshanskaya / Alexey A Alekseev / Laura Y Yen / Shanti Pal Gangwar / Ivan A Sobolevsky / Maria G Kurnikova / Alexander I Sobolevsky /
Abstract: AMPA receptors (AMPARs) mediate fast excitatory neurotransmission. Gating of AMPARs starts with agonist binding and transition into a non-conducting pre-active state, followed by transition into ...AMPA receptors (AMPARs) mediate fast excitatory neurotransmission. Gating of AMPARs starts with agonist binding and transition into a non-conducting pre-active state, followed by transition into conducting open or non-conducting desensitized states. While the terminal apo, open and desensitized states have been structurally characterized, the intermediate pre-active state has remained an enigma. Compared to full agonist glutamate, partial agonists reduce the maximal occupancy of the open state and increase the probability of the pre-active state occurrence. Here we use different partial agonists and time-resolved cryo-electron microscopy (cryo-EM) to capture a structural ensemble of GluA2-γ2 AMPAR complexes in the closed apo, pre-active, open and desensitized states. Binding of partial agonists to the ligand-binding domain (LBD) results in different extents of LBD clamshell closure, with closures exceeding a threshold of ~17° resulting in the open and desensitized states and smaller closures stabilizing the pre-active state. The pre-active state has a distinct gate conformation intermediate between the other two discrete states, completely open and closed. Combined with single-channel current recordings and molecular dynamics simulations, our structural results reveal the complete gating pathway of AMPARs and shed light on the molecular mechanisms of partial agonism and pre-activation.
History
DepositionMar 15, 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_76105.png

Downloads & links

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Map

FileDownload / File: emd_76105.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationATD
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 400 pix.
= 323.6 Å		0.81 Å/pix.
x 400 pix.
= 323.6 Å		0.81 Å/pix.
x 400 pix.
= 323.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.809 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.3349101 - 0.57868594
Average (Standard dev.)0.0012814287 (±0.014080868)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 323.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half a

Fileemd_76105_half_map_1.map
Annotationhalf a
Projections & Slices
AxesZYX

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Histogram

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Half map: half b

Fileemd_76105_half_map_2.map
Annotationhalf b
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Sample components

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Entire : GluA2-STZ pre-active state with partial agonist kainic acid (KA) ...

EntireName: GluA2-STZ pre-active state with partial agonist kainic acid (KA) at 25 degrees C (ATD only)
Components
  • Complex: GluA2-STZ pre-active state with partial agonist kainic acid (KA) at 25 degrees C (ATD only)

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Supramolecule #1: GluA2-STZ pre-active state with partial agonist kainic acid (KA) ...

SupramoleculeName: GluA2-STZ pre-active state with partial agonist kainic acid (KA) at 25 degrees C (ATD 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 uMC10H15NO4kainic acid (KA)

Details: 150 mM NaCl, 20 mM Tris-HCl pH 8.0, and 0.05% digitonin, 250 uM KA
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 500 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER
DetailsMonodisperse, multiview particles

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.64 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: 5876023
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: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 133149
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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