[English] 日本語
Yorodumi
- EMDB-67447: LY334370-bound serotonin 1F (5-HT1F) receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-67447
TitleLY334370-bound serotonin 1F (5-HT1F) receptor
Map data
Sample
  • Complex: GPCR bound with a ligand
    • Protein or peptide: 5-hydroxytryptamine receptor 1F
  • Ligand: 4-fluoranyl-~{N}-[3-(1-methylpiperidin-4-yl)-1~{H}-indol-5-yl]benzamide
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Gi/o-coupled serotonin receptor activity / serotonin receptor activity / Serotonin receptors / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / serotonin binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / adenylate cyclase-inhibiting serotonin receptor signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G alpha (i) signalling events ...Gi/o-coupled serotonin receptor activity / serotonin receptor activity / Serotonin receptors / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / serotonin binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / adenylate cyclase-inhibiting serotonin receptor signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G alpha (i) signalling events / chemical synaptic transmission / synapse / dendrite / plasma membrane
Similarity search - Function
5-Hydroxytryptamine 1F receptor / 5-hydroxytryptamine receptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
5-hydroxytryptamine receptor 1F
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsCao C / Ji Z / Wang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)GG9100007022 China
CitationJournal: Biochem Biophys Res Commun / Year: 2026
Title: Structural basis of LY334370 recognition and selectivity at the 5-HT receptor.
Authors: Yumeng Wang / Chunyu Wang / Can Cao /
Abstract: The 5-HT receptor is a serotonin receptor subtype highly expressed in trigeminal sensory neurons, where it modulates neuropeptide release and nociceptive signaling without inducing vasoconstriction. ...The 5-HT receptor is a serotonin receptor subtype highly expressed in trigeminal sensory neurons, where it modulates neuropeptide release and nociceptive signaling without inducing vasoconstriction. This makes it an important therapeutic target for migraine. LY334370 was developed as a first-generation selective 5-HTR agonist and demonstrated efficacy in clinical studies. However, the molecular mechanism underlying 5-HTR activation by LY334370 remains poorly understood. Here, we determined a 3.13 Å cryo-EM structure of the LY334370-bound 5-HTR-miniGα complex. Combined with functional analyses, this structure delineates the molecular determinants underlying LY334370 recognition. Comparison with BRL54443 indicates that LY334370 selectivity for 5-HTR is driven by its optimal accommodation within the receptor-specific extended binding pocket. Furthermore, comparative analysis with the lasmiditan-bound 5-HTR-Gα complex reveals distinct agonist binding modes and provides mechanistic insight into Gα subtype-specific coupling. Collectively, these findings elucidate the structural basis of 5-HTR activation, ligand selectivity, and G protein coupling, providing a structural framework for the rational design of safer and more effective anti-migraine drugs.
History
DepositionDec 4, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_67447.png

Downloads & links

-
Map

FileDownload / File: emd_67447.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 352 pix.
= 288.64 Å		0.82 Å/pix.
x 352 pix.
= 288.64 Å		0.82 Å/pix.
x 352 pix.
= 288.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.115
Minimum - Maximum-0.497417 - 0.7944113
Average (Standard dev.)-0.00009432175 (±0.008658858)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 288.63998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_67447_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_67447_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GPCR bound with a ligand

EntireName: GPCR bound with a ligand
Components
  • Complex: GPCR bound with a ligand
    • Protein or peptide: 5-hydroxytryptamine receptor 1F
  • Ligand: 4-fluoranyl-~{N}-[3-(1-methylpiperidin-4-yl)-1~{H}-indol-5-yl]benzamide

-
Supramolecule #1: GPCR bound with a ligand

SupramoleculeName: GPCR bound with a ligand / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.71 KDa

-
Macromolecule #1: 5-hydroxytryptamine receptor 1F

MacromoleculeName: 5-hydroxytryptamine receptor 1F / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.76198 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDFLNSSDQN LTSEELLNRM PSKILVSLTL SGLALMTTTI NSLVIAAIIV TRKLHHPANY LICSLAVTDF LVAVLVMPFS IVYIVRESW IMGQVVCDIW LSVDITCCTC SILHLSAIAL DRYRAITDAV EYARKRTPKH AGIMITIVWI ISVFISMPPL F WRHQGTSR ...String:
MDFLNSSDQN LTSEELLNRM PSKILVSLTL SGLALMTTTI NSLVIAAIIV TRKLHHPANY LICSLAVTDF LVAVLVMPFS IVYIVRESW IMGQVVCDIW LSVDITCCTC SILHLSAIAL DRYRAITDAV EYARKRTPKH AGIMITIVWI ISVFISMPPL F WRHQGTSR DDECIIKHDH IVSTIYSTFG AFYIPLALIL ILYYKIYRAA KTLYHKRQAS RIAKEEVNGQ VLLESGEKST KS VSTSYVL EKSLSDPSTD FDKIHSTVRS LRSEFKHEKS WRRQKISGTR ERKAATTLGL ILGAFVICWL PFFVKELVVN VCD KCKISE EMSNFLAWLG YLNSLINPLI YTIFNEDFKK AFQKLVRCRC

UniProtKB: 5-hydroxytryptamine receptor 1F

-
Macromolecule #2: 4-fluoranyl-~{N}-[3-(1-methylpiperidin-4-yl)-1~{H}-indol-5-yl]ben...

MacromoleculeName: 4-fluoranyl-~{N}-[3-(1-methylpiperidin-4-yl)-1~{H}-indol-5-yl]benzamide
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1E2G
Molecular weightTheoretical: 351.417 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7exd

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 114556
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more