9JG0 | pdb_00009jg0

Cryo-EM structure of neuropeptide FF receptor 2 in the ligand-free state with BRIL fusion, anti-BRIL Fab, and nanobody


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9JG0

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: 122.74 kDa 
  • Atom Count: 7,271 
  • Modeled Residue Count: 950 
  • Deposited Residue Count: 1,101 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of Neuropeptide FF receptor 2,Soluble cytochrome b562A [auth R]526Homo sapiensEscherichia coliMutation(s): 0 
Gene Names: NPFFR2GPR74NPFF2NPGPRcybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for Q9Y5X5 (Homo sapiens)
Explore Q9Y5X5 
Go to UniProtKB:  Q9Y5X5
PHAROS:  Q9Y5X5
GTEx:  ENSG00000056291 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9Y5X5P0ABE7
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Anti-BRIL fab heavy chainB [auth H]229Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Anti-fab nanobodyC [auth K]131synthetic constructMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Anti-BRIL fab light chainD [auth L]215Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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: 2025-07-02
    Changes: Data collection