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- EMDB-41796: CDPPB, QUS bound mGlu5 in complex with Nb43, non uniform refineme... -

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Basic information

Entry
Database: EMDB / ID: EMD-41796
TitleCDPPB, QUS bound mGlu5 in complex with Nb43, non uniform refinement of the whole complex
Map datasharpened map of CDPPB, QUS bound mGlu5 in complex with Nb43, non-uniform refinement of the whole complex
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: 2.93 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 30, 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_41796.png

Downloads & links

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Map

FileDownload / File: emd_41796.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, non-uniform refinement of 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: 0.242
Minimum - Maximum-2.7250524 - 4.144109
Average (Standard dev.)0.00015728896 (±0.059715286)
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_41796_half_map_1.map
Annotationhalf map of CDPPB, QUS bound mGlu5 in complex with Nb43, non-uniform refinement of 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 CDPPB, QUS bound mGlu5 in...

Fileemd_41796_half_map_2.map
Annotationhalf map of CDPPB, QUS bound mGlu5 in complex with Nb43, non-uniform refinement of 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 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: 2.93 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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