9VI9 | pdb_00009vi9

Cryo-EM Structure of NPFFR1 in complex with peptide RFRP-3

• PDB DOI: https://doi.org/10.2210/pdb9VI9/pdb
• EM Map EMD-65081: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2025-06-17 Released: 2025-12-03 
• Deposition Author(s): Na, M., Xu, F.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.02 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Molecular recognition at the opioid-modulating neuropeptide FF receptor 1.

Na, M., Yue, Y., Xu, K., Xu, Z., Zhang, L., Zhou, F., De Neve, J., Ballet, S., Xu, F.

(2026) Protein Cell 17: 372-377

• PubMed: 41206054 
• DOI: https://doi.org/10.1093/procel/pwaf090
• Primary Citation Related Structures: 
  9VI9, 9VIF

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Organizational Affiliation: 
• iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China, 201210.
Shanghai Academy of Natural Sciences (SANS), Shanghai, China, 200032.
Research Group of Organic Chemistry, Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 145.76 kDa 
• Atom Count: 9,025 
• Modeled Residue Count: 1,149 
• Deposited Residue Count: 1,308 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropeptide FF receptor 1	A	310	Homo sapiens	Mutation(s): 0  Gene Names: NPFFR1, GPR147, NPFF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZQ6 (Homo sapiens) Explore Q9GZQ6  Go to UniProtKB:  Q9GZQ6
PHAROS:  Q9GZQ6 GTEx:  ENSG00000148734

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	349	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	338	Homo sapiens	Mutation(s): 0  Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873  Go to UniProtKB:  P62873
PHAROS:  P62873 GTEx:  ENSG00000078369

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	54	Homo sapiens	Mutation(s): 0  Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RFRP-3	E [auth P]	9	Homo sapiens	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	F [auth S]	248	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.02 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Na, M., Xu, F.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release
  
• Version 1.1: 2026-05-06
  Changes: Data collection, Database references