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- EMDB-41807: QUS bounds mGlu5 in complex with Nb43, non uniform refinement on ... -

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Basic information

Entry
Database: EMDB / ID: EMD-41807
TitleQUS bounds mGlu5 in complex with Nb43, non uniform refinement on the whole complex
Map datasharpened map of QUS bound inactive mGlu5 in complex with Nb43, non uniform refinement on the whole complex
Sample
  • Organelle or cellular component: Metabotropic glutamate receptor 5 in complex with Quis
KeywordsGPCR / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsKrishna Kumar K / Wang H / Kobilka BK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS028471 United States
CitationJournal: Nature / Year: 2024
Title: Stepwise activation of a metabotropic glutamate receptor.
Authors: Kaavya Krishna Kumar / Haoqing Wang / Chris Habrian / Naomi R Latorraca / Jun Xu / Evan S O'Brien / Chensong Zhang / Elizabeth Montabana / Antoine Koehl / Susan Marqusee / Ehud Y Isacoff / Brian K Kobilka /
Abstract: Metabotropic glutamate receptors belong to a family of G protein-coupled receptors that are obligate dimers and possess a large extracellular ligand-binding domain that is linked via a cysteine-rich ...Metabotropic glutamate receptors belong to a family of G protein-coupled receptors that are obligate dimers and possess a large extracellular ligand-binding domain that is linked via a cysteine-rich domain to their 7-transmembrane domain. Upon activation, these receptors undergo a large conformational change to transmit the ligand binding signal from the extracellular ligand-binding domain to the G protein-coupling 7-transmembrane domain. In this manuscript, we propose a model for a sequential, multistep activation mechanism of metabotropic glutamate receptor subtype 5. We present a series of structures in lipid nanodiscs, from inactive to fully active, including agonist-bound intermediate states. Further, using bulk and single-molecule fluorescence imaging, we reveal distinct receptor conformations upon allosteric modulator and G protein binding.
History
DepositionAug 31, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41807.png

Downloads & links

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Map

FileDownload / File: emd_41807.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map of QUS bound inactive mGlu5 in complex with Nb43, non uniform refinement on the whole complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 340 pix.
= 377.74 Å		1.11 Å/pix.
x 340 pix.
= 377.74 Å		1.11 Å/pix.
x 340 pix.
= 377.74 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.111 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.206
Minimum - Maximum-2.1720417 - 3.0598452
Average (Standard dev.)0.0004476125 (±0.035567764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 377.74 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map of QUS bound inactive mGlu5 in...

Fileemd_41807_half_map_1.map
Annotationhalf map of QUS bound inactive mGlu5 in complex with Nb43, non uniform refinement on the whole complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of QUS bound inactive mGlu5 in...

Fileemd_41807_half_map_2.map
Annotationhalf map of QUS bound inactive mGlu5 in complex with Nb43, non uniform refinement on the whole complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Metabotropic glutamate receptor 5 in complex with Quis

EntireName: Metabotropic glutamate receptor 5 in complex with Quis
Components
  • Organelle or cellular component: Metabotropic glutamate receptor 5 in complex with Quis

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Supramolecule #1: Metabotropic glutamate receptor 5 in complex with Quis

SupramoleculeName: Metabotropic glutamate receptor 5 in complex with Quis
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

0346

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 211019
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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