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- PDB-9yfu: Structure of GPR61 bound to inverse agonist compound 15 -

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Basic information

Entry
Database: PDB / ID: 9yfu
TitleStructure of GPR61 bound to inverse agonist compound 15
Components
  • Fab24 BAK5 heavy chain
  • Fab24 BAK5 light chain
  • G-protein coupled receptor 61,Soluble cytochrome b562
  • Hinge-binding nanobody
KeywordsSIGNALING PROTEIN / GPCR / GPR61 / orphan receptor / inverse agonist
Function / homology
Function and homology information


ligand-independent adenylate cyclase-activating G protein-coupled receptor signaling pathway / arrestin family protein binding / electron transport chain / G protein-coupled receptor activity / periplasmic space / electron transfer activity / signaling receptor complex / endosome membrane / endosome / iron ion binding ...ligand-independent adenylate cyclase-activating G protein-coupled receptor signaling pathway / arrestin family protein binding / electron transport chain / G protein-coupled receptor activity / periplasmic space / electron transfer activity / signaling receptor complex / endosome membrane / endosome / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / plasma membrane
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
: / Soluble cytochrome b562 / G-protein coupled receptor 61
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsLees, J.A. / Dias, J.M. / Han, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2026
Title: Discovery of Potent and Brain-Penetrant Inverse Agonists for GPR61, an Orphan G Protein-Coupled Receptor.
Authors: Fisher, E.L. / Dechert Schmitt, A.M. / Tuttle, J.B. / Unwalla, R. / Lovett, G.H. / Kormos, B.L. / Coffman, K.J. / Zhou, D. / Moran, M. / Williams, J. / Xiao, J. / LaChapelle, E.A. / Fortin, ...Authors: Fisher, E.L. / Dechert Schmitt, A.M. / Tuttle, J.B. / Unwalla, R. / Lovett, G.H. / Kormos, B.L. / Coffman, K.J. / Zhou, D. / Moran, M. / Williams, J. / Xiao, J. / LaChapelle, E.A. / Fortin, J.P. / Sheikh, A.Q. / Stevens, K.A. / Kong, J.X. / Hughes, E.A.G. / Esquejo, R.M. / Joaquim, S. / Amar, N.L. / Archambault, D. / Garren, J. / Breen, D. / Jagarlapudi, S. / Dullea, R. / O'Connor, R.E. / Koslov-Davino, E. / Callegari, E. / Dias, J.M. / Lees, J.A. / Borzilleri, K. / Han, S. / Brooks, J. / Vajdos, F.F. / Goyal, A. / Zhang, L. / Zhang, Y.
History
DepositionSep 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: G-protein coupled receptor 61,Soluble cytochrome b562
H: Fab24 BAK5 heavy chain
N: Hinge-binding nanobody
C: Fab24 BAK5 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,1795
Polymers127,7244
Non-polymers4551
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 1 molecules R

#1: Protein G-protein coupled receptor 61,Soluble cytochrome b562 / Biogenic amine receptor-like G-protein coupled receptor / Cytochrome b-562


Mass: 59860.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPR61, BALGR, GPCR3, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9BZJ8, UniProt: P0ABE7

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Antibody , 3 types, 3 molecules HNC

#2: Antibody Fab24 BAK5 heavy chain


Mass: 24021.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody Hinge-binding nanobody


Mass: 14957.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Antibody Fab24 BAK5 light chain


Mass: 28884.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-A1CWB / N-(5-chloro-4,6-dimethylpyrimidin-2-yl)-6-{[(3,5-difluoropyridin-4-yl)methyl]amino}-2-methylpyridine-3-sulfonamide


Mass: 454.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17ClF2N6O2S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of GPR61 ICL3 BRIL fusion with Fab24 BAK5 and Fab hinge-binding nanobody bound to inverse agonist compound 15
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
2PHENIX1.19_4092model refinement
13cryoSPARC3.3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266475 / Symmetry type: POINT
RefinementHighest resolution: 3.08 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037040
ELECTRON MICROSCOPYf_angle_d0.5739574
ELECTRON MICROSCOPYf_dihedral_angle_d4.533984
ELECTRON MICROSCOPYf_chiral_restr0.041086
ELECTRON MICROSCOPYf_plane_restr0.0061228

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