9M2F | pdb_00009m2f

Structure of neuropeptide FF receptor 1 complex with NPFF


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 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
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1A [auth B]366Rattus norvegicusMutation(s): 0 
Gene Names: Gnb1
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UniProt GroupP54311
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2B [auth G]71Bos taurusMutation(s): 0 
Gene Names: GNG2
UniProt
Find proteins for P63212 (Bos taurus)
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
neuropeptide FFC [auth L]8synthetic constructMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1D [auth A]354Homo sapiensMutation(s): 2 
Gene Names: GNAI1
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Neuropeptide FF receptor 1,Neuropeptide FF receptor 1,LgbitE [auth R]536Homo sapienssynthetic construct
This entity is chimeric
Mutation(s): 0 
Gene Names: NPFFR1GPR147NPFF1
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PHAROS:  Q9GZQ6
GTEx:  ENSG00000148734 
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UniProt GroupQ9GZQ6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
scfv16F [auth S]247synthetic constructMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC
RECONSTRUCTIONcryoSPARC
RECONSTRUCTIONcryoSPARC

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