9VI9: NPFFR1

Cryo-EM Structure of NPFFR1 in complex with peptide RFRP-3. Determined by electron microscopy at 3.02 Å resolution. Released 3 Dec 2025.

Method: Electron microscopy
Resolution: 3.02 Å
Organism: Homo sapiens
Chains: 6
Atoms: 9,025
Mol. weight: 145.76 kDa
Released: 3 Dec 2025

Explore 9VI9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9VI9 contains 30 α-helices and 69 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	30	1
β-strand	31-34	4	1
β-strand	36	1	2
α-helix	40-70	31
α-helix	77-105	29
β-strand	106	1	2
α-helix	113-146	34
α-helix	151-153	3
α-helix	155-179	25
β-strand	180-184	5	3
β-strand	188-191	4	1
β-strand	197-198	2	1
β-strand	201-205	5	3
α-helix	210-212	3
α-helix	213-221	9
α-helix	222-226	5
α-helix	227-245	19
α-helix	260-295	36
α-helix	300-305	6
α-helix	306-310	5
α-helix	311-330	20

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-39	6	4
α-helix	46-53	8
β-strand	185-190	6	4
β-strand	195-200	6	4
α-helix	208-215	8
β-strand	220-225	6	4
β-strand	233	1	5
β-strand	241	1	5
α-helix	242-254	13
β-strand	263-268	6	4
α-helix	274-280	7
α-helix	296-309	14
β-strand	319-323	5	4
α-helix	331-350	20

Chain C: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	30-33	4
α-helix	38-39	2
β-strand	43	1	6
β-strand	47-51	5	7
β-strand	58-63	6	8
β-strand	69-74	6	8
β-strand	78-83	6	8
β-strand	89-94	6	8
β-strand	100-105	6	9
β-strand	111-116	6	9
β-strand	120-125	6	9
β-strand	134-140	7	9
β-strand	146-153	8	10
β-strand	156-161	6	10
β-strand	165-170	6	10
β-strand	176-181	6	10
β-strand	187-192	6	11
β-strand	198-203	6	11
β-strand	208-212	5	11
β-strand	218-222	5	11
β-strand	229-232	4	12
β-strand	240-245	6	12
β-strand	250-254	5	12
β-strand	260-264	5	12
β-strand	273-278	6	6
α-helix	280-282	3
β-strand	284-289	6	6
β-strand	294-298	5	6
β-strand	304-308	5	6
β-strand	315-320	6	7
β-strand	327-331	5	7
β-strand	336-339	4	7

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	40-51	12
α-helix	52-55	4
α-helix	61-69	9

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3

Chain S: 1 helix, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	11	1	14
β-strand	18-24	7	13
α-helix	29-31	3
β-strand	33-39	7	15
β-strand	45-51	7	15
β-strand	58-60	3	15
β-strand	68-73	6	13
β-strand	78-83	6	13
β-strand	92-99	8	15
β-strand	110-111	2	15
β-strand	115-117	3	15
β-strand	118	1	14
β-strand	140	1	16
β-strand	146	1	17
β-strand	155-159	5	18
β-strand	161	1	16
β-strand	174-179	6	19
β-strand	186-189	4	19
β-strand	191	1	20
β-strand	194	1	20
β-strand	203-204	2	18
β-strand	212-216	5	18
β-strand	226-231	6	19
β-strand	238	1	15
β-strand	244	1	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropeptide FF receptor 1	A	protein	310	Homo sapiens	Q9GZQ6 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	protein	349	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	338	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	54	Homo sapiens	P59768 (AlphaFold model)
Rfrp-3	P	protein	9	Homo sapiens
scFv16	S	protein	248	Homo sapiens

Sequence of entity 1 (A), FASTA

>9VI9_1 Neuropeptide FF receptor 1 (chains A)
NLTFSSYYQHTSPVAAMFIVAYALIFLLCMVGNTLVCFIVLKNRHMHTVTNMFILNLAVS
DLLVGIFCMPTTLVDNLITGWPFDNATCKMSGLVQGMSVSASVWTLVAIAVERFRCIVHP
FREKLTLRKALVTIAVIWALALLIMCPSAVTLTVTREEHHFMVDARNRSYPLYSCWEAWP
EKGMRRVYTTVLFSHIYLAPLALIVVMYARIARKLCQAPGPAPGGEEAADPRASRRRARV
VHMLVMVALFFTLSWLPLWALLLLIDYGQLSAPQLHLVTVYAFPFAHWLAFFNSSANPII
YGYFNENFRR

Sequence of entity 2 (B), FASTA

>9VI9_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
SAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAGYSEEE
CKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAG
VIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTGIV
ETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHE
SMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQC
QFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (C), FASTA

>9VI9_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
ELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMH
WGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICS
IYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTG
HTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFA
TGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKA
DRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (D), FASTA

>9VI9_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF

Sequence of entity 5 (P), FASTA

>9VI9_5 RFRP-3 (chains P)
VPNLPQRFA

Sequence of entity 6 (S), FASTA

>9VI9_6 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Primary citation

Molecular recognition at the opioid-modulating neuropeptide FF receptor 1. Na, M., Yue, Y., Xu, K. et al. Protein Cell (2026) 17:372-377. DOI 10.1093/procel/pwaf090 · PubMed

Other PDB entries of the same protein (UniProt Q9GZQ6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9M0R 2.47 Å, Structure of neuropeptide FF receptor 1 complex with NPVF
9M2F 2.93 Å, Structure of neuropeptide FF receptor 1 complex with NPFF
9VIF 3.19 Å, Cryo-EM Structure of NPFFR1 in complex with peptide NPFF

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