9KFJ: PDB entry 9KFJ

Cryo-EM structure of the compound 4-bound human relaxin family peptide receptor 3 (RXFP3)-Gi complex. Determined by electron microscopy at 3.1 Å resolution. Released 13 Aug 2025.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Escherichia coli, Homo sapiens, synthetic construct
Chains: 5
Atoms: 8,948
Mol. weight: 195.06 kDa
Ligands: IYF
Released: 13 Aug 2025

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

Secondary structure: helices and β-sheets

9KFJ contains 36 α-helices and 62 β-strands across 5 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 C: 15 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	80-108	29
α-helix	112-114	3
α-helix	116-133	18
α-helix	135-143	9
β-strand	148	1	1
α-helix	153-185	33
α-helix	214-234	21
β-strand	239-240	2	1
β-strand	245-246	2	1
α-helix	270-271	2
α-helix	272-276	5
α-helix	277-298	22
α-helix	313-317	5
α-helix	318-354	37
α-helix	359-363	5
α-helix	364-379	16
α-helix	381-390	10
α-helix	394-403	10

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-41	12
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain I: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-40	7	2
α-helix	46-53	8
β-strand	186-192	7	2
β-strand	195-201	7	2
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-227	7	2
α-helix	243-255	13
α-helix	258-260	3
β-strand	264-270	7	2
α-helix	272-279	8
α-helix	284-286	3
α-helix	297-309	13
β-strand	320-323	4	2
α-helix	332-352	21

Chain S: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	3
β-strand	11-12	2	4
β-strand	17-24	8	3
α-helix	29-31	3
β-strand	33-39	7	5
β-strand	45-51	7	5
β-strand	59-60	2	5
β-strand	68-73	6	3
α-helix	74-76	3
β-strand	78-84	7	3
α-helix	88-90	3
β-strand	93-94	2	6
β-strand	95-99	5	5
β-strand	111	1	5
β-strand	115-116	2	6
β-strand	118-119	2	4
α-helix	138-140	3
β-strand	141	1	7
β-strand	146-148	3	8
β-strand	155-160	6	7
β-strand	166	1	9
β-strand	172	1	9
β-strand	174-179	6	8
β-strand	186-189	4	8
β-strand	203-207	5	7
β-strand	211-216	6	7
β-strand	225-231	7	8
β-strand	239	1	8
β-strand	243-246	4	8

Chain T: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	6-25	20
α-helix	30-33	4
β-strand	47-51	5	10
β-strand	58-63	6	11
β-strand	69-74	6	11
β-strand	78-83	6	11
β-strand	88-94	7	11
β-strand	100-105	6	12
β-strand	111-116	6	12
β-strand	121-125	5	12
β-strand	134-139	6	12
β-strand	146-151	6	13
β-strand	156-161	6	13
β-strand	165-170	6	13
β-strand	175-181	7	13
β-strand	187-192	6	14
β-strand	198-203	6	14
β-strand	208-212	5	14
β-strand	218-222	5	14
β-strand	229-234	6	15
β-strand	240-245	6	15
β-strand	249-254	6	15
β-strand	259-264	6	15
β-strand	273-277	5	16
β-strand	284-289	6	16
β-strand	294-298	5	16
β-strand	304-308	5	16
β-strand	315-320	6	10
β-strand	327-331	5	10
β-strand	336-339	4	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,Relaxin-3 receptor 1,LgBiT	C	protein	773	Escherichia coli, Homo sapiens, synthetic construct	Q9NSD7 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	55	Homo sapiens	P59768 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-2	I	protein	355	Homo sapiens	P04899 (AlphaFold model)
scFv16	S	protein	247	synthetic construct
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	T	protein	338	Homo sapiens	P62873 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>9KFJ_1 Soluble cytochrome b562,Relaxin-3 receptor 1,LgBiT (chains C)
MKTIIALSYIFCLVFAHHHHHHHHHHADLEDNWETLNDNLKVIEKADNAAQVKDALTKMR
AAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQL
KTTRNAYIQKYLQMADAATIATMNKAAGGDKLAELFSLVPDLLEAANTSGNASLQLPDLW
WELGLELPDGAPPGHPPGSGGAESADTEARVRILISVVYWVVCALGLAGNLLVLYLMKSM
QGWRKSSINLFVTNLALTDFQFVLTLPFWAVENALDFKWPFGKAMCKIVSMVTSMNMYAS
VFFLTAMSVTRYHSVASALKSHRTRGHGRGDCCGRSLGDSCCFSAKALCVWIWALAALAS
LPSAIFSTTVKVMGEELCLVRFPDKLLGRDRQFWLGLYHSQKVLLGFVLPLGIIILCYLL
LVRFIADRRAAGTKGGAAVAGGRPTGASARRLSKVTKSVTIVVLSFFLCWLPNQALTTWS
ILIKFNAVPFSQEYFLCQVYAFPVSVCLAHSNSCLNPVLYCLVRREFRKALKSLLWRIAS
PSITSMRPFTATTKPEHEDQGLQAPAPPHAAAEPDLLYYPPGVVVYSGGRYDLLPSSSAY
GSSGGGGSGGGGSSGVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRI
VRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTP
NMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINS

Sequence of entity 2 (G), FASTA

>9KFJ_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 3 (I), FASTA

>9KFJ_3 Guanine nucleotide-binding protein G(i) subunit alpha-2 (chains I)
MGCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEDG
YSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPSRADDARQLFALSCTAEEQGVL
PDDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYIPTQQDVLRTRV
KTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEE
MNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGANKYDEA
ASYIQSKFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (S), FASTA

>9KFJ_4 scFv16 (chains S)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Sequence of entity 5 (T), FASTA

>9KFJ_5 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains T)
ELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMH
WGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICS
IYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTG
HTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFA
TGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKA
DRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Ligands and cofactors

ID	Name	Formula	Copies
IYF	1-[2-(4-chlorophenyl)ethyl]-3-[(7-ethyl-5-oxidanyl-1H-indol-3-yl)methylideneami…	C20 H22 Cl N5 O	1

Primary citation

Molecular mechanism underlying non-discriminatory recognition of relaxin-3 by RXFP3 and RXFP4. Chen, Y., Zhou, Q., Yan, S. et al. Commun Biol (2025) 8:794-794. DOI 10.1038/s42003-025-08220-7 · PubMed

Other PDB entries of the same protein (UniProt Q9NSD7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9KFI 2.91 Å, Cryo-EM structure of the human relaxin family peptide receptor 3 in complex with…

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