9M1O | pdb_00009m1o

Cryo-EM structures of NPFFR2 complex with neuropeptide FF


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of peptide recognition and modulation for neuropeptide FF receptors.

Li, X.Zhang, H.Hu, W.Wu, K.Li, S.Jin, S.Yin, Y.Yuan, Q.Xu, H.E.Pan, B.Jiang, Y.

(2025) Cell Rep 44: 116160-116160

  • DOI: https://doi.org/10.1016/j.celrep.2025.116160
  • Primary Citation of Related Structures:  
    9M0R, 9M1O, 9M2F, 9M54

  • PubMed Abstract: 

    Neuropeptide FF receptors 1 and 2 (NPFFR1 and NPFFR2) are RF-amide peptide receptors that couple to G i/o proteins and regulate pain, opioid tolerance, and metabolism. Despite their physiological significance, their ligand selectivity and activation mechanisms remain unclear. Using cryoelectron microscopy, we resolved four NPFFR1 and NPFFR2 structures bound to NPFF or NPVF, revealing conserved C-terminal RF-amide interactions within the orthosteric pocket and N-terminal variations driving subtype specificity. Structural and mutagenesis analyses identified ECL2 and the receptor N terminus as key determinants of NPVF-NPFFR1 and NPFF-NPFFR2 selectivity. Additionally, the structures elucidate the activation mechanism and uncover distinct G i -coupling features between NPFFR subtypes. These findings provide molecular insights into peptide recognition and receptor activation within the RF-amide family, offering a structural framework for designing selective NPFFR modulators to treat pain, addiction, and metabolic disorders with enhanced specificity and reduced off-target effects.


  • Organizational Affiliation
    • School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Lingang Laboratory, Shanghai, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Neuropeptide FF receptor 2,Neuropeptide FF receptor 2A [auth R]589Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: cybCNPFFR2GPR74NPFF2NPGPR
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PHAROS:  Q9Y5X5
GTEx:  ENSG00000056291 
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UniProt GroupQ9Y5X5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1366Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Bos taurusMutation(s): 0 
Gene Names: GNG2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Morphine-modulating neuropeptide BD [auth L]9synthetic constructMutation(s): 1 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scfv16E [auth S]247synthetic constructMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1F [auth A]354Homo sapiensMutation(s): 2 
Gene Names: GNAI1
EC: 3.6.5
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Find proteins for P63096 (Homo sapiens)
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GTEx:  ENSG00000127955 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Data collection, Database references