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- PDB-8yjp: Cryo-EM structure of human apo GPR156 -

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Basic information

Entry
Database: PDB / ID: 8yjp
TitleCryo-EM structure of human apo GPR156
ComponentsProbable G-protein coupled receptor 156
KeywordsMEMBRANE PROTEIN / GPCR / class C / GPR156 / cryo-EM / homodimer
Function / homology
Function and homology information


stereocilium bundle organization / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / gamma-aminobutyric acid signaling pathway / plasma membrane
Similarity search - Function
GPR156, 7TM domain / GPCR family 3, GABA-B receptor / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR
Similarity search - Domain/homology
CHOLESTEROL / Chem-MW9 / Probable G-protein coupled receptor 156
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsMa, X.Y. / Chen, L.N. / Liao, M.H. / Zhang, L.Y. / Xi, K. / Guo, J.M.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Nat Commun / Year: 2024
Title: Molecular insights into the activation mechanism of GPR156 in maintaining auditory function.
Authors: Xiangyu Ma / Li-Nan Chen / Menghui Liao / Liyan Zhang / Kun Xi / Jiamin Guo / Cangsong Shen / Dan-Dan Shen / Pengjun Cai / Qingya Shen / Jieyu Qi / Huibing Zhang / Shao-Kun Zang / Ying-Jun ...Authors: Xiangyu Ma / Li-Nan Chen / Menghui Liao / Liyan Zhang / Kun Xi / Jiamin Guo / Cangsong Shen / Dan-Dan Shen / Pengjun Cai / Qingya Shen / Jieyu Qi / Huibing Zhang / Shao-Kun Zang / Ying-Jun Dong / Luwei Miao / Jiao Qin / Su-Yu Ji / Yue Li / Jianfeng Liu / Chunyou Mao / Yan Zhang / Renjie Chai /
Abstract: The class C orphan G-protein-coupled receptor (GPCR) GPR156, which lacks the large extracellular region, plays a pivotal role in auditory function through G. Here, we firstly demonstrate that GPR156 ...The class C orphan G-protein-coupled receptor (GPCR) GPR156, which lacks the large extracellular region, plays a pivotal role in auditory function through G. Here, we firstly demonstrate that GPR156 with high constitutive activity is essential for maintaining auditory function, and further reveal the structural basis of the sustained role of GPR156. We present the cryo-EM structures of human apo GPR156 and the GPR156-G complex, unveiling a small extracellular region formed by extracellular loop 2 (ECL2) and the N-terminus. The GPR156 dimer in both apo state and G protein-coupled state adopt a transmembrane (TM)5/6-TM5/6 interface, indicating the high constitutive activity of GPR156 in the apo state. Furthermore, C-terminus in G-bound subunit of GPR156 plays a dual role in promoting G protein binding within G-bound subunit while preventing the G-free subunit from binding to additional G protein. Together, these results explain how GPR156 constitutive activity is maintained through dimerization and provide a mechanistic insight into the sustained role of GPR156 in maintaining auditory function.
History
DepositionMar 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable G-protein coupled receptor 156
B: Probable G-protein coupled receptor 156
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,53315
Polymers76,9442
Non-polymers6,58813
Water00
1


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

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Components

#1: Protein Probable G-protein coupled receptor 156 / G-protein coupled receptor PGR28 / GABAB-related G-protein coupled receptor


Mass: 38472.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPR156, GABABL, PGR28 / Production host: Homo sapiens (human) / References: UniProt: Q8NFN8
#2: Chemical
ChemComp-MW9 / (21R,24R,27S)-24,27,28-trihydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaoctacosan-21-yl (9Z)-octadec-9-enoate / 1-stearoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol)


Mass: 777.060 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H81O10P
#3: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C27H46O
Has ligand of interestN
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: GPR156 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164823 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045066
ELECTRON MICROSCOPYf_angle_d0.7016915
ELECTRON MICROSCOPYf_dihedral_angle_d12.008824
ELECTRON MICROSCOPYf_chiral_restr0.047872
ELECTRON MICROSCOPYf_plane_restr0.006768

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