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- EMDB-65621: The structure of odorant-bound mouse class II odorant receptor-mi... -

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Basic information

Entry
Database: EMDB / ID: EMD-65621
TitleThe structure of odorant-bound mouse class II odorant receptor-miniGs complex
Map dataComposite map
Sample
  • Complex: Complex of Odorant-bound Olfr412 and heterotrimeric G protein
    • Complex: mini G
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha
    • Complex: G protein
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: nanobody
      • Protein or peptide: Nanobody 35
    • Complex: receptor
      • Protein or peptide: Olfactory receptor
  • Ligand: Methyl cinnamate
KeywordsOdorant receptor / MEMBRANE PROTEIN / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Olfactory Signaling Pathway / olfactory receptor activity / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway ...Olfactory Signaling Pathway / olfactory receptor activity / G protein-coupled receptor activity / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / sensory perception of smell / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex / G alpha (12/13) signalling events / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / sensory perception of taste / Thrombin signalling through proteinase activated receptors (PARs) / signaling receptor complex adaptor activity / retina development in camera-type eye / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Ras protein signal transduction / Extra-nuclear estrogen signaling / cell population proliferation / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / GTP binding / protein-containing complex binding / signal transduction / extracellular exosome / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Olfactory receptor / Olfactory receptor / G-protein alpha subunit, group S / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. ...Olfactory receptor / Olfactory receptor / G-protein alpha subunit, group S / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(s) subunit alpha / Olfactory receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChoi CW / Gil MS / Choi 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_65621.png

Downloads & links

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Map

FileDownload / File: emd_65621.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite 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: 0.12
Minimum - Maximum-0.5686767 - 1.1344534
Average (Standard dev.)0.0026636382 (±0.015290332)
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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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
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha
    • Complex: G protein
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: nanobody
      • Protein or peptide: Nanobody 35
    • Complex: receptor
      • Protein or peptide: Olfactory receptor
  • Ligand: Methyl cinnamate

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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: G protein

SupramoleculeName: G protein / 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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Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.051812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSNSKTEDQR NEEKAQREAN KKIEKQLQKD KQVYRATHRL LLLGADNSGK STIVKQMRIL HGGSGGSGGT SGIFETKFQV DKVNFHMFD VGGQRDERRK WIQCFNDVTA IIFVVDSSDY NRLQEALNLF KSIWNNRWLR TISVILFLNK QDLLAEKVLA G KSKIEDYF ...String:
GSNSKTEDQR NEEKAQREAN KKIEKQLQKD KQVYRATHRL LLLGADNSGK STIVKQMRIL HGGSGGSGGT SGIFETKFQV DKVNFHMFD VGGQRDERRK WIQCFNDVTA IIFVVDSSDY NRLQEALNLF KSIWNNRWLR TISVILFLNK QDLLAEKVLA G KSKIEDYF PEFARYTTPE DATPEPGEDP RVTRAKYFIR DEFLRISTAS GDGRHYCYPH FTCAVDTENA RRIFNDCRDI IQ RMHLRQY ELL

UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha, Guanine nucleotide-binding protein G(s) subunit alpha

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.418086 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR ...String:
MHHHHHHLEV LFQGPGSSGS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLV SASQDGKLII WDSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG H TGYLSCCR FLDDNQIVTS SGDTTCALWD IETGQQTTTF TGHTGDVMSL SLAPDTRLFV SGACDASAKL WDVREGMCRQ TF TGHESDI NAICFFPNGN AFATGSDDAT CRLFDLRADQ ELMTYSHDNI ICGITSVSFS KSGRLLLAGY DDFNCNVWDA LKA DRAGVL AGHDNRVSCL GVTDDGMAVA TGSWDSFLKI WN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #4: Nanobody 35

MacromoleculeName: Nanobody 35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.273889 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VQLQESGGGL VQPGGSLRLS CAASGFTFSN YKMNWVRQAP GKGLEWVSDI SQSGASISYT GSVKGRFTIS RDNAKNTLYL QMNSLKPED TAVYYCARCP APFTRDCFDV TSTTYAYRGQ GTQVTVHHHH H

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Macromolecule #5: Olfactory receptor

MacromoleculeName: Olfactory receptor / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 35.201219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDGGNQSGDS EFLLLGLSEV PEHQRILFWT FLSMYLVTVV GNVLIILAIG SDSHLHTPMY FFLANLSFTD LFFVTNTIPK MLVSLQSQN KAISYPGCLT QLFFLVSLVA LDNLILAVMA YDRYVAICHP LHYTTAMSPK LCILLLILCW ALSILYGLIH T LLMTRVTF ...String:
MDGGNQSGDS EFLLLGLSEV PEHQRILFWT FLSMYLVTVV GNVLIILAIG SDSHLHTPMY FFLANLSFTD LFFVTNTIPK MLVSLQSQN KAISYPGCLT QLFFLVSLVA LDNLILAVMA YDRYVAICHP LHYTTAMSPK LCILLLILCW ALSILYGLIH T LLMTRVTF CGSRKIHYIF CEMYVLLRLA CSNTHINHMM LIATGCFVFL VPFGFMIMSY ICIVRAILKI PSASNKYKAF ST CASHLAV VALFYGTLCM VYLKPVHTYS MKDSVATVMY AVVTPMMNPF IYSLRNKDMH GALGRLLRKP LQKLT

UniProtKB: Olfactory receptor

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Macromolecule #6: Methyl cinnamate

MacromoleculeName: Methyl cinnamate / type: ligand / ID: 6 / Number of copies: 1 / Formula: A1MBB
Molecular weightTheoretical: 162.185 Da

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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

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