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- EMDB-63638: octopamine b2 receptor with bound octopamine -

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Basic information

Entry
Database: EMDB / ID: EMD-63638
Titleoctopamine b2 receptor with bound octopamine
Map data
Sample
  • Complex: octopamine b2 receptor and Gs complex with agonist
    • Complex: octopamine
      • Protein or peptide: octopamine b2 receptor with bound octopamine
    • 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 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 ...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 / 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 / ADP signalling through P2Y purinoceptor 1 / cellular response to catecholamine stimulus / 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 / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (12/13) signalling events / 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 / cytosol / cytoplasm
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) / Ixodes scapularis bunyavirus / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 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 beta2 receptor.
Authors: Hori T / Katsuta K / Miyamoto-Kohno S / Uchikubo-Kamo T / Yonemochi M / Shirouzu M
History
DepositionMar 5, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63638.png

Downloads & links

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Map

FileDownload / File: emd_63638.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 °

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Supplemental data

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Half map: #1

Fileemd_63638_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_63638_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 : octopamine b2 receptor and Gs complex with agonist

EntireName: octopamine b2 receptor and Gs complex with agonist
Components
  • Complex: octopamine b2 receptor and Gs complex with agonist
    • Complex: octopamine
      • Protein or peptide: octopamine b2 receptor with bound octopamine
    • 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

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Supramolecule #1: octopamine b2 receptor and Gs complex with agonist

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

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Supramolecule #2: octopamine

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

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Macromolecule #1: octopamine b2 receptor with bound octopamine

MacromoleculeName: octopamine b2 receptor with bound octopamine / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Ixodes scapularis bunyavirus
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

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Macromolecule #2: G-protein alpha subunit

MacromoleculeName: G-protein alpha subunit / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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

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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

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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

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Macromolecule #5: single chain Fv 16

MacromoleculeName: single chain Fv 16 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: 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

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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: 7.5
VitrificationCryogen name: ETHANE

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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

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 410720
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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