9JFY | pdb_00009jfy

Cryo-EM structure of Neuropeptide FF receptor 2 in complex with hNPSF and Gi


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural insights into the selective recognition of RF-amide peptides by neuropeptide FF receptor 2.

Kim, J.Hong, S.Lee, H.Lee, H.S.Park, C.Kim, J.Im, W.Choi, H.J.

(2025) EMBO Rep 26: 2413-2434

  • DOI: https://doi.org/10.1038/s44319-025-00428-2
  • Primary Citation Related Structures: 
    9JFY, 9JG0

  • PubMed Abstract: 

    Neuropeptide FF Receptor 2 (NPFFR2), a G-protein-coupled receptor, plays a role in pain modulation and diet-induced thermogenesis. While NPFFR2 is strongly activated by neuropeptides FF (NPFFs), it shows low activity in response to RF-amide-related peptides (RFRPs), despite the peptides belonging to a shared family. In contrast, NPFFR1, which shares high sequence similarity with NPFFR2, is activated by RFRPs and regulates reproductive hormone balance. The molecular basis for these receptor-specific interactions with their RF-amide peptides remains unclear. Here, we present cryo-electron microscopy structures of NPFFR2 in its active state bound to the agonist RF-amide peptide hNPSF, and in its ligand-free state. Structural analysis reveals that the C-terminal RF-amide moiety engages conserved residues in the transmembrane domain, while the N-terminal segment interacts in a receptor subtype-specific manner. Key selectivity-determining residues in NPFFR2 are also identified. A homology model of NPFFR1 bound to RFRP, supported by mutagenesis studies, further validates this selectivity mechanism. Additionally, structural comparison between the inactive and active states of NPFFR2 suggests a TM3-mediated activation mechanism. These findings provide insights into RF-amide peptide recognition by NPFF receptors.


  • Organizational Affiliation
    • Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 164.87 kDa 
  • Atom Count: 8,805 
  • Modeled Residue Count: 1,134 
  • Deposited Residue Count: 1,470 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of Neuropeptide FF receptor 2A [auth R]429Homo sapiensMutation(s): 0 
Gene Names: NPFFR2GPR74NPFF2NPGPR
Membrane Entity: Yes 
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Find proteins for Q9Y5X5 (Homo sapiens)
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PHAROS:  Q9Y5X5
GTEx:  ENSG00000056291 
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UniProt GroupQ9Y5X5
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Neuropeptide SFB [auth L]12Homo sapiensMutation(s): 1 
Membrane Entity: Yes 
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GTEx:  ENSG00000139574 
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UniProt GroupO15130
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1C [auth A]354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
Membrane Entity: Yes 
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Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1D [auth B]345Homo sapiensMutation(s): 0 
Gene Names: GNB1
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GTEx:  ENSG00000078369 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2E [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
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GTEx:  ENSG00000186469 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
single-chain antibody Fv fragment (scFv16)F [auth S]259Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Data collection, Database references
  • Version 1.2: 2025-06-18
    Changes: Data collection