9JG0: PDB entry 9JG0

Cryo-EM structure of neuropeptide FF receptor 2 in the ligand-free state with BRIL fusion, anti-BRIL Fab, and nanobody. Determined by electron microscopy at 2.91 Å resolution. Released 9 Apr 2025.

Method: Electron microscopy
Resolution: 2.91 Å
Organisms: Homo sapiens, Escherichia coli, synthetic construct
Chains: 4
Atoms: 7,271
Mol. weight: 122.74 kDa
Released: 9 Apr 2025

Explore 9JG0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JG0 contains 36 α-helices and 61 β-strands across 4 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 H: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	3
β-strand	14-15	2	4
β-strand	20-28	9	3
β-strand	35-42	8	5
β-strand	48-55	8	5
β-strand	60-63	4	5
β-strand	71-76	6	3
β-strand	81-87	7	3
α-helix	91-93	3
β-strand	95-103	9	5
α-helix	108-111	4
β-strand	116-117	2	5
β-strand	118	1	3
β-strand	121-123	3	5
β-strand	124-125	2	4
β-strand	131	1	6
β-strand	134-138	5	7
β-strand	149-159	11	7
β-strand	160	1	6
β-strand	165-168	4	8
α-helix	169-171	3
β-strand	173	1	8
β-strand	177-179	3	7
α-helix	180-182	3
β-strand	183-184	2	7
β-strand	190-199	10	7
α-helix	200-205	6
β-strand	208-213	6	8
β-strand	214	1	9
α-helix	215-217	3
β-strand	219	1	9
β-strand	222-225	4	8

Chain K: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-11	2	11
β-strand	16-25	10	10
β-strand	33-39	7	11
β-strand	46-51	6	11
β-strand	58-60	3	11
β-strand	68-73	6	10
β-strand	78-86	9	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	108-110	3	11
β-strand	115-118	4	11

Chain L: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	12
β-strand	11-14	4	13
β-strand	20-26	7	12
β-strand	34-39	6	13
β-strand	46-50	5	13
β-strand	54-55	2	13
α-helix	56	1
β-strand	63-68	6	12
β-strand	71-76	6	12
α-helix	81-83	3
β-strand	86-94	9	13
β-strand	97-99	3	13
β-strand	104-108	5	13
α-helix	114-115	2
β-strand	116-120	5	14
α-helix	121-123	3
α-helix	124-127	4
β-strand	131-141	11	14
β-strand	147-152	6	15
β-strand	156	1	15
β-strand	161-165	5	14
α-helix	166-169	4
β-strand	175-184	10	14
α-helix	185-189	5
β-strand	193-199	7	15
β-strand	207-212	6	15

Chain R: 22 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	33-36	4	1
β-strand	38	1	2
α-helix	42-72	31
α-helix	79-97	19
α-helix	99-107	9
β-strand	108	1	2
α-helix	115-148	34
α-helix	153-156	4
α-helix	157-174	18
α-helix	176-180	5
β-strand	183-193	11	1
β-strand	200-207	8	1
α-helix	213-223	11
α-helix	224-229	6
α-helix	230-269	40
α-helix	273-292	20
α-helix	311-331	21
α-helix	335-342	8
α-helix	344-347	4
α-helix	348-352	5
α-helix	353-395	43
α-helix	401-406	6
α-helix	407-411	5
α-helix	412-421	10
α-helix	422-424	3
α-helix	426-432	7
α-helix	435-448	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Neuropeptide FF receptor 2,Soluble cytochrome b562	R	protein	526	Homo sapiens, Escherichia coli	P0ABE7 (AlphaFold model), Q9Y5X5 (AlphaFold model)
Anti-BRIL fab heavy chain	H	protein	229	Homo sapiens
Anti-fab nanobody	K	protein	131	synthetic construct
Anti-BRIL fab light chain	L	protein	215	Homo sapiens

Sequence of entity 1 (R), FASTA

>9JG0_1 Isoform 2 of Neuropeptide FF receptor 2,Soluble cytochrome b562 (chains R)
DYKDDDDASSENWHPIWNVNDTKHHLYSDINITYVNYYLHQPQVAAIFIISYFLIFFLCM
MGNTVVCFIVMRNKHMHTVTNLFILNLAISDLLVGIFCMPITLLDNIIAGWPFGNTMCKI
SGLVQGISVAASVFTLVAIAVDRFQCVVYPFKPKLTIKTAFVIIMIIWVLAITIMSPSAV
MLHVQEEKYYRVRLNSQNKTSPVYWCREDWPNQEMRKIYTTVLFANIYLAPLSLIVIMYG
RIGISARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLED
KSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERAR
STLRKKQKIIKMLLIVALLFILSWLPLWTLMMLSDYADLSPNELQIINIYIYPFAHWLAF
GNSSVNPIIYGFFNENFRRGFQEAFQLQLCQKRAKPMEAYALKAKSHVLINTSNQLVQES
TFQNPHGETLLYRKSAEKPQQELVMEELKETTNSSEIHMGLEVLFQ

Sequence of entity 2 (H), FASTA

>9JG0_2 Anti-BRIL fab heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Sequence of entity 3 (K), FASTA

>9JG0_3 Anti-fab nanobody (chains K)
GSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGA
FYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVT
VSSLEHHHHHH

Sequence of entity 4 (L), FASTA

>9JG0_4 Anti-BRIL fab light chain (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIF
PPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Primary citation

Structural insights into the selective recognition of RF-amide peptides by neuropeptide FF receptor 2. Kim, J., Hong, S., Lee, H. et al. EMBO Rep (2025) 26:2413-2434. DOI 10.1038/s44319-025-00428-2 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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