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- EMDB-65619: Globally refined map of odorant-bound mouse class II odorant rece... -

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Basic information

Entry
Database: EMDB / ID: EMD-65619
TitleGlobally refined map of odorant-bound mouse class II odorant receptor G protein complex
Map dataMain sharp map
Sample
  • Complex: Complex of Odorant-bound Olfr412 and heterotrimeric G protein
    • Complex: mini G
    • Complex: Gprotein
    • Complex: nanobody
    • Complex: receptor
KeywordsOdorant receptor / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human) / Lama glama (llama) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChoi CW / Gil MS / Chio H-J
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
Samsung Science and Technology Foundation Korea, Republic Of
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: The structure of odorant-bound mouse class II odorant receptor-miniGs complex
Authors: Choi CW / Gil MS / Choi H-J
History
DepositionJul 30, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65619.png

Downloads & links

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Map

FileDownload / File: emd_65619.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain sharp map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.73591596 - 1.2120495
Average (Standard dev.)0.000028686445 (±0.017345207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: non-sharp map

Fileemd_65619_additional_1.map
Annotationnon-sharp map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_65619_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_65619_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Odorant-bound Olfr412 and heterotrimeric G protein

EntireName: Complex of Odorant-bound Olfr412 and heterotrimeric G protein
Components
  • Complex: Complex of Odorant-bound Olfr412 and heterotrimeric G protein
    • Complex: mini G
    • Complex: Gprotein
    • Complex: nanobody
    • Complex: receptor

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Supramolecule #1: Complex of Odorant-bound Olfr412 and heterotrimeric G protein

SupramoleculeName: Complex of Odorant-bound Olfr412 and heterotrimeric G protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5

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Supramolecule #2: mini G

SupramoleculeName: mini G / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Gprotein

SupramoleculeName: Gprotein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: nanobody

SupramoleculeName: nanobody / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Lama glama (llama)

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Supramolecule #5: receptor

SupramoleculeName: receptor / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Mus musculus (house mouse)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 94056
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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