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- EMDB-41789: TM region local refinement of CDPPB, QUS bound mGlu5 in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-41789
TitleTM region local refinement of CDPPB, QUS bound mGlu5 in complex with Nb43
Map datasharpened map of CDPPB, QUS bound mGlu5 in complex with Nb43, local refinement on the TM region
Sample
  • Organelle or cellular component: Metabotropic glutamate receptor 5 bound to Quis and CDPPB, in complex with Nb43
KeywordsGPCR / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.46 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: To Be Published
Title: Quis and CDPPB bound active mGlu5
Authors: Krishna Kumar K / Wang H / Kobilka BK
History
DepositionAug 29, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41789.png

Downloads & links

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Map

FileDownload / File: emd_41789.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map of CDPPB, QUS bound mGlu5 in complex with Nb43, local refinement on the TM region
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-0.84451914 - 1.2734864
Average (Standard dev.)0.00009589184 (±0.017847864)
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 CDPPB, QUS bound mGlu5 in...

Fileemd_41789_half_map_1.map
Annotationhalf map of CDPPB, QUS bound mGlu5 in complex with Nb43, local refinement on the TM region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of CDPPB, QUS bound mGlu5 in...

Fileemd_41789_half_map_2.map
Annotationhalf map of CDPPB, QUS bound mGlu5 in complex with Nb43, local refinement on the TM region
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 bound to Quis and CDPPB, in com...

EntireName: Metabotropic glutamate receptor 5 bound to Quis and CDPPB, in complex with Nb43
Components
  • Organelle or cellular component: Metabotropic glutamate receptor 5 bound to Quis and CDPPB, in complex with Nb43

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Supramolecule #1: Metabotropic glutamate receptor 5 bound to Quis and CDPPB, in com...

SupramoleculeName: Metabotropic glutamate receptor 5 bound to Quis and CDPPB, in complex with Nb43
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: 51.6 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

Startup modelType of model: EMDB MAP
EMDB ID:

0346

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 245439
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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