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- PDB-8xqj: Cryo-EM structure of human dimeric APJR complex with antagonistic... -

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Basic information

Entry
Database: PDB / ID: 8xqj
TitleCryo-EM structure of human dimeric APJR complex with antagonistic antibody
Components
  • JN241
  • Soluble cytochrome b562,Apelin receptor
KeywordsSIGNALING PROTEIN / GPCR / APJR / Antibody / Antagonist / JN241
Function / homology
Function and homology information


: / apelin receptor activity / apelin receptor signaling pathway / mechanoreceptor activity / regulation of gap junction assembly / positive regulation of G protein-coupled receptor internalization / vascular associated smooth muscle cell differentiation / atrioventricular valve development / regulation of body fluid levels / venous blood vessel development ...: / apelin receptor activity / apelin receptor signaling pathway / mechanoreceptor activity / regulation of gap junction assembly / positive regulation of G protein-coupled receptor internalization / vascular associated smooth muscle cell differentiation / atrioventricular valve development / regulation of body fluid levels / venous blood vessel development / positive regulation of cardiac muscle hypertrophy in response to stress / endocardial cushion formation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / coronary vasculature development / adult heart development / vasculature development / G protein-coupled peptide receptor activity / aorta development / negative regulation of cardiac muscle hypertrophy in response to stress / ventricular septum morphogenesis / blood vessel development / heart looping / vasculogenesis / gastrulation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / electron transport chain / G protein-coupled receptor activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of angiogenesis / signaling receptor activity / heart development / regulation of gene expression / angiogenesis / G alpha (i) signalling events / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding / negative regulation of gene expression / heme binding / plasma membrane
Similarity search - Function
Apelin receptor / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
CHOLESTEROL / Soluble cytochrome b562 / Apelin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsYue, Y. / Liu, L.E. / Wu, L.J. / Xu, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into the regulation of monomeric and dimeric apelin receptor.
Authors: Yang Yue / Lier Liu / Lijie Wu / Chanjuan Xu / Man Na / Shenhui Liu / Yuxuan Liu / Fei Li / Junlin Liu / Songting Shi / Hui Lei / Minxuan Zhao / Tianjie Yang / Wei Ji / Arthur Wang / Michael ...Authors: Yang Yue / Lier Liu / Lijie Wu / Chanjuan Xu / Man Na / Shenhui Liu / Yuxuan Liu / Fei Li / Junlin Liu / Songting Shi / Hui Lei / Minxuan Zhao / Tianjie Yang / Wei Ji / Arthur Wang / Michael A Hanson / Raymond C Stevens / Jianfeng Liu / Fei Xu /
Abstract: The apelin receptor (APJR) emerges as a promising drug target for cardiovascular health and muscle regeneration. While prior research unveiled the structural versatility of APJR in coupling to Gi ...The apelin receptor (APJR) emerges as a promising drug target for cardiovascular health and muscle regeneration. While prior research unveiled the structural versatility of APJR in coupling to Gi proteins as a monomer or dimer, the dynamic regulation within the APJR dimer during activation remains poorly understood. In this study, we present the structures of the APJR dimer and monomer complexed with its endogenous ligand apelin-13. In the dimeric structure, apelin-13 binds exclusively to one protomer that is coupled with Gi proteins, revealing a distinct ligand-binding behavior within APJR homodimers. Furthermore, binding of an antagonistic antibody induces a more compact dimerization by engaging both protomers. Notably, structural analyses of the APJR dimer complexed with an agonistic antibody, with or without Gi proteins, suggest that G protein coupling may promote the dissociation of the APJR dimer during activation. These findings underscore the intricate interplay between ligands, dimerization, and G protein coupling in regulating APJR signaling pathways.
History
DepositionJan 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.0Jan 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 22, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 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: JN241
B: JN241
C: Soluble cytochrome b562,Apelin receptor
D: Soluble cytochrome b562,Apelin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8768
Polymers144,3294
Non-polymers1,5474
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody JN241


Mass: 17852.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Protein Soluble cytochrome b562,Apelin receptor / Cytochrome b-562 / Angiotensin receptor-like 1 / G-protein coupled receptor APJ / G-protein coupled ...Cytochrome b-562 / Angiotensin receptor-like 1 / G-protein coupled receptor APJ / G-protein coupled receptor HG11


Mass: 54312.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: cybC, APLNR, AGTRL1, APJ / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0ABE7, UniProt: P35414
#3: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / 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: APJR complex with antibody / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.4
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: 2200 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170746 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037090
ELECTRON MICROSCOPYf_angle_d0.569660
ELECTRON MICROSCOPYf_dihedral_angle_d3.875990
ELECTRON MICROSCOPYf_chiral_restr0.0391104
ELECTRON MICROSCOPYf_plane_restr0.0051164

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