[English] 日本語
Yorodumi
- EMDB-63636: Octopamine receptor b2 with bound DPMF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63636
TitleOctopamine receptor b2 with bound DPMF
Map data
Sample
  • Complex: octopamine b2 receptor and Gs complex with DPMF
    • Complex: DPMF
      • Protein or peptide: octopamine b2 receptor
    • Protein or peptide: G-protein alpha subunit
    • Protein or peptide: G-protein beta subunit
    • Protein or peptide: G-protein gamma subunit
    • Protein or peptide: single chain Fv 16
KeywordsGPCR / SIGNALING PROTEIN
Function / homology
Function and homology information


Olfactory Signaling Pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation ...Olfactory Signaling Pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / G beta:gamma signalling through BTK / photoreceptor disc membrane / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / 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 / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / 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 / 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 / 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 / protein-containing complex binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 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 ...G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / 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
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesIxodes scapularis (black-legged tick) / Homo sapiens (human) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHori T / Katsuta K / Shirouzu M
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K05046 Japan
CitationJournal: PNAS Nexus / Year: 2025
Title: Structural insights into endogenous agonist selectivity of aminergic receptors from the octopamine β receptor.
Authors: Tetsuya Hori / Kazushige Katsura / Sayako Miyamoto-Kohno / Tomomi Uchikubo-Kamo / Mayumi Yonemochi / Mikako Shirouzu /
Abstract: Tyrosine-derived amines (TDAs), such as octopamine, noradrenaline, dopamine, and tyramine, are essential neurotransmitters that play diverse roles in various physiological processes. The distinct ...Tyrosine-derived amines (TDAs), such as octopamine, noradrenaline, dopamine, and tyramine, are essential neurotransmitters that play diverse roles in various physiological processes. The distinct receptor selectivity of these structurally similar molecules is vital for their specific functions. However, all these receptors belong to the same subfamily of G-protein-coupled receptors and share high sequence homology within their orthosteric binding sites. The molecular basis of this selectivity remains unclear because of the absence of structural data on octopamine and tyramine receptors. In this study, we present cryo-electron microscopy structures of the deer tick octopamine β receptor (octβR) bound to octopamine or -2,4-dimethylphenyl-'-methylformamidine (DPMF), an acaricidal amitraz metabolite. Octopamine and DPMF formed aromatic interactions with Y307 and F328, residues crucial for octβR activation. The lower potency of other TDAs for octβR stems from the subtle effect of functional groups on both interactions, i.e. the meta-hydroxyl group of noradrenaline and dopamine hinders edge-to-edge interaction with Y307, and the absence of a 1-hydroxyl group in dopamine and tyramine prevents π-hydrogen bonding with F328. These structural insights into octβR selectivity are likely applicable across other TDA receptors, highlighting the pivotal role of residues 6.55 and 7.39. Consequently, the elucidated selection mechanism provides fundamental knowledge of aminergic ligand recognition, a process crucial for neurotransmission and overall organismal function.
History
DepositionMar 5, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63636.png

Downloads & links

-
Map

FileDownload / File: emd_63636.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 256 pix.
= 212.096 Å		0.83 Å/pix.
x 256 pix.
= 212.096 Å		0.83 Å/pix.
x 256 pix.
= 212.096 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8285 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-35.038573999999997 - 49.839466000000002
Average (Standard dev.)0.000000000003224 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.096 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_63636_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_63636_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : octopamine b2 receptor and Gs complex with DPMF

EntireName: octopamine b2 receptor and Gs complex with DPMF
Components
  • Complex: octopamine b2 receptor and Gs complex with DPMF
    • Complex: DPMF
      • Protein or peptide: octopamine b2 receptor
    • Protein or peptide: G-protein alpha subunit
    • Protein or peptide: G-protein beta subunit
    • Protein or peptide: G-protein gamma subunit
    • Protein or peptide: single chain Fv 16

-
Supramolecule #1: octopamine b2 receptor and Gs complex with DPMF

SupramoleculeName: octopamine b2 receptor and Gs complex with DPMF / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ixodes scapularis (black-legged tick)

-
Supramolecule #2: DPMF

SupramoleculeName: DPMF / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

-
Macromolecule #1: octopamine b2 receptor

MacromoleculeName: octopamine b2 receptor / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Ixodes scapularis (black-legged tick)
Recombinant expressionOrganism: Spodoptera frugiperda granulovirus
SequenceString: MKTIIALSYI FCLVFADYKD DDDKENLYFQ GMTVAAPNAS LANLTEEAQA DDESWESVLK LVLKTLALVT IISSAVFGNL LVVTSVIRHH KLRITTNYFI VSLALADTLV ALFAMTFNAS VTISGRWLFN QTVCDFWNSC DVLFSTASIM HLCCISVDRY YAIIKPLEYP ...String:
MKTIIALSYI FCLVFADYKD DDDKENLYFQ GMTVAAPNAS LANLTEEAQA DDESWESVLK LVLKTLALVT IISSAVFGNL LVVTSVIRHH KLRITTNYFI VSLALADTLV ALFAMTFNAS VTISGRWLFN QTVCDFWNSC DVLFSTASIM HLCCISVDRY YAIIKPLEYP TKITGRTVAI MLTCAWVSSG LISFIPIFLG WYTTNEHLVY KVEHPDECIF VVNKPYAIIS SSVSFWIPCC IMLFTYWRIY VEATRQEKML CKSQMGPGML CRNSTDQSMP NVHAPPHRNS HGDDPESGQS TPTKRTINKM KREHKAAKTL GIIMGAFILC WLPFFLWYVS ITMCGDACPC PELVVDLLFW IGYLNSSLNP VIYAYFNREF RQAFKETLQA IFCSSRCSSC ATGSRQTGGR PPGRTHHHHH HHHHH

-
Macromolecule #2: G-protein alpha subunit

MacromoleculeName: G-protein alpha subunit / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Ixodes scapularis (black-legged tick)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKDHLIHNHH KHEHAHAEHL YFQGSSGSSG MASTLSAEDK AAVERSKMIE KQIQKDKQIY RATHRLLLLG AGESGKNTIV KQMRILHVNG FSEEEKKQKI EDIKKNIRDA ILTITGAMST LVPPVQLQKS ENQWRVDYIQ DVASSPDFDY PAEFYEHTEI LWKDKGVQAA ...String:
MKDHLIHNHH KHEHAHAEHL YFQGSSGSSG MASTLSAEDK AAVERSKMIE KQIQKDKQIY RATHRLLLLG AGESGKNTIV KQMRILHVNG FSEEEKKQKI EDIKKNIRDA ILTITGAMST LVPPVQLQKS ENQWRVDYIQ DVASSPDFDY PAEFYEHTEI LWKDKGVQAA FERSNEYQLI DCAKYFLDRV ATIKQLDYTP NEQDILRCRV LTSGIFETKF QVDKVNFHMF DVGAQRDERR KWIQCFNDVT AIIFVTACSS YNMVLREDPN QNRLRASLKL FDSIWNNKWL RDTSVILFLN KQDLLAEKIK AGKSRLEEYF PEFAHYQTPS DAVIETGEDP EVIRAKYFIR DEFLRISTAS GDGKHYCYPH FTCSVDTENI RRVFNDCRDI IQRMHLRQYE LL

-
Macromolecule #3: G-protein beta subunit

MacromoleculeName: G-protein beta subunit / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda granulovirus
SequenceString: mdykddddke nlyfqggsMS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLVS ASQDGKLIIW DSYTTNKVHA IPLRSSWVMT CAYAPSGNYV ACGGLDNICS IYNLKTREGN VRVSRELAGH TGYLSCCRFL ...String:
mdykddddke nlyfqggsMS ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLVS ASQDGKLIIW DSYTTNKVHA IPLRSSWVMT CAYAPSGNYV ACGGLDNICS IYNLKTREGN VRVSRELAGH TGYLSCCRFL DDNQIVTSSG DTTCALWDIE TGQQTTTFTG HTGDVMSLSL APDTRLFVSG ACDASAKLWD VREGMCRQTF TGHESDINAI CFFPNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRVSCLGVTD DGMAVATGSW DSFLKIWN

-
Macromolecule #4: G-protein gamma subunit

MacromoleculeName: G-protein gamma subunit / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda granulovirus
SequenceString:
msyyhhhhhh dydipttenl yfqgamgsMA SNNTASIAQA RKLVEQLKME ANIDRIKVSK AAADLMAYCE AHAKEDPLLT PVPASENPFR EKKFFSAIL

-
Macromolecule #5: single chain Fv 16

MacromoleculeName: single chain Fv 16 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString: MKDHLIHNHH KHEHAHAEHL YFQGSSGSSG DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS SGGGGSGGGG SGGGGSDIVM ...String:
MKDHLIHNHH KHEHAHAEHL YFQGSSGSSG DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS SGGGGSGGGG SGGGGSDIVM TQATSSVPVT PGESVSISCR SSKSLLHSNG NTYLYWFLQR PGQSPQLLIY RMSNLASGVP DRFSGSGSGT AFTLTISRLE AEDVGVYYCM QHLEYPLTFG AGTKLELKSA WSHPQFEKGG GSGGGSGGSA WSHPQFEK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 246183
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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