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- EMDB-65169: Cryo-EM structure of the spermine-bound sea lamprey TAAR348-Gs complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65169
TitleCryo-EM structure of the spermine-bound sea lamprey TAAR348-Gs complex
Map data
Sample
  • Complex: The spermine-bound sea lamprey TAAR348-Gs complex
    • Protein or peptide: Trace amine-associated receptor 12707.TAAR348
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • 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
    • Protein or peptide: Nb35
    • Protein or peptide: scFv16
KeywordsGPCR / TAAR348 / Spermine / Sea lamprey / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli) / Petromyzon marinus (sea lamprey) / Homo sapiens (human) / Lama glama (llama) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsJiang KX / Zheng Y / Xu F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2025
Title: Chemosensation of the pheromone spermine by the olfactory TAAR-like receptor TAAR348.
Authors: Kexin Jiang / Liting Zeng / Weifeng Zhang / Xuefei He / You Zheng / Ling Wang / Zhongyuan Zhang / Jun Pu / Cheng Deng / Fan Yang / Suwen Zhao / Fei Xu /
History
DepositionJun 26, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65169.png

Downloads & links

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Map

FileDownload / File: emd_65169.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.161
Minimum - Maximum-0.9884637 - 1.4264506
Average (Standard dev.)-0.0005426924 (±0.035171002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65169_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65169_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The spermine-bound sea lamprey TAAR348-Gs complex

EntireName: The spermine-bound sea lamprey TAAR348-Gs complex
Components
  • Complex: The spermine-bound sea lamprey TAAR348-Gs complex
    • Protein or peptide: Trace amine-associated receptor 12707.TAAR348
    • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • 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
    • Protein or peptide: Nb35
    • Protein or peptide: scFv16

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Supramolecule #1: The spermine-bound sea lamprey TAAR348-Gs complex

SupramoleculeName: The spermine-bound sea lamprey TAAR348-Gs complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Trace amine-associated receptor 12707.TAAR348

MacromoleculeName: Trace amine-associated receptor 12707.TAAR348 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Petromyzon marinus (sea lamprey)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKHHHHHH HHHHLEVLFQ GPADLEDNWE TLNDNLKVIE KADNAAQVK DALTKMRAAA LDAQKATPPK LEDKSPDSPE MKDFRHGFDI LVGQIDDALK L ANEGKVKE AQAAAEQLKT TRNAYIQKYL MGQPGNGSAM SSHANTTSPA ...String:
MKTIIALSYI FCLVFADYKD DDDKHHHHHH HHHHLEVLFQ GPADLEDNWE TLNDNLKVIE KADNAAQVK DALTKMRAAA LDAQKATPPK LEDKSPDSPE MKDFRHGFDI LVGQIDDALK L ANEGKVKE AQAAAEQLKT TRNAYIQKYL MGQPGNGSAM SSHANTTSPA CGLTFYDFNC SR ASVTSSS ERAQVMSLLL SISAITIAGN LLTITSILYF RQLQTRTNVL TLSLAVADLL VGL LIMPFS VMRSVHNCWF YGRVFCRVHT WLDYTFCTSS IVHLSCISFD RYVAISDPLR YEQR VTRRA CVRMLVCCWL CLLVYGLAFM MEWNLVGLEE EVAHICPDDC PVLLNLPFAM ANTIF ACIV PMMLMTLAYG RIYQLARQQA RKITSAAVGS NADSARSSLR REHSATITMG IIVGVF ISL WIPYFVVSVT EPIFGYHASS VTWEVINWFT YINSTANPIL FAAFNRPFRN AFYLILS GR MFASSCRGVD LFDVLRALAK ARG

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Macromolecule #2: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSTVSAEDK AAAERSKMID KNLREDGEKA AAATHRLLLL GADNSGKSTI VKQMRILHGG SGGSGGTSG IFETKFQVDK VNFHMFDVGG QRDERRKWIQ CFNDVTAIIF VVDSSDYNRL Q EALNLFKS IWNNRWLRTI SVILFLNKQD LLAEKVLAGK SKIEDYFPEF ...String:
MGSTVSAEDK AAAERSKMID KNLREDGEKA AAATHRLLLL GADNSGKSTI VKQMRILHGG SGGSGGTSG IFETKFQVDK VNFHMFDVGG QRDERRKWIQ CFNDVTAIIF VVDSSDYNRL Q EALNLFKS IWNNRWLRTI SVILFLNKQD LLAEKVLAGK SKIEDYFPEF ARYTTPEDAT PE PGEDPRV TRAKYFIRDE FLRISTASGD GRHYCYPHFT CAVDTENARR IFNDCRDIIQ RMH LRQYEL L

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Macromolecule #3: 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: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN

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Macromolecule #4: 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: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

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Macromolecule #5: Nb35

MacromoleculeName: Nb35 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Recombinant expressionOrganism: Escherichia (bacteria)
SequenceString:
MQVQLQESGG GLVQPGGSLR LSCAASGFTF SNYKMNWVRQ APGKGLEWVS DISQSGASIS YTGSVKGRFT ISRDNAKNTL YLQMNSLKP EDTAVYYCAR CPAPFTRDCF DVTSTTYAYR GQGTQVTVSS HHHHHHEPEA

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Macromolecule #6: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFADV QLVESGGGLV QPGGSRKLSC SASGFAFSS FGMHWVRQAP EKGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL Q MTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS SGGGGSGGGG ...String:
MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFADV QLVESGGGLV QPGGSRKLSC SASGFAFSS FGMHWVRQAP EKGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL Q MTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS SGGGGSGGGG SGGGGSDIVM TQ ATSSVPV TPGESVSISC RSSKSLLHSN GNTYLYWFLQ RPGQSPQLLI YRMSNLASGV PDR FSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FGAGTKLELK AAAHHHHHHH H

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 269228
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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