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- EMDB-65165: Cryo-EM structure of the spermine-bound sea lamprey TAAR348 -

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Basic information

Entry
Database: EMDB / ID: EMD-65165
TitleCryo-EM structure of the spermine-bound sea lamprey TAAR348
Map data
Sample
  • Complex: The spermine-bound TAAR348
    • Protein or peptide: Trace amine-associated receptor 12707.TAAR348
KeywordsGPCR / TAAR348 / Spermine / Sea lamprey / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli) / Petromyzon marinus (sea lamprey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 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_65165.png

Downloads & links

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Map

FileDownload / File: emd_65165.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: 0.1
Minimum - Maximum-0.29344818 - 0.5005338
Average (Standard dev.)-0.00052160217 (±0.010057562)
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_65165_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_65165_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 TAAR348

EntireName: The spermine-bound TAAR348
Components
  • Complex: The spermine-bound TAAR348
    • Protein or peptide: Trace amine-associated receptor 12707.TAAR348

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Supramolecule #1: The spermine-bound TAAR348

SupramoleculeName: The spermine-bound TAAR348 / 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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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: 3.26 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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