9KFI: Human relaxin family peptide receptor 3

Cryo-EM structure of the human relaxin family peptide receptor 3 in complex with relaxin-3 and G protein. Determined by electron microscopy at 2.91 Å resolution. Released 13 Aug 2025.

Method: Electron microscopy
Resolution: 2.91 Å
Organisms: Escherichia coli, Homo sapiens, synthetic construct
Chains: 7
Atoms: 9,293
Mol. weight: 199.76 kDa
Released: 13 Aug 2025

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

Secondary structure: helices and β-sheets

9KFI contains 40 α-helices and 69 β-strands across 7 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-10	9

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	13-21	9

Chain C: 16 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	80-103	24
α-helix	104-109	6
α-helix	116-133	18
α-helix	135-143	9
α-helix	152-185	34
α-helix	220-227	8
α-helix	230-234	5
β-strand	236	1	1
β-strand	239-240	2	2
β-strand	245-246	2	2
β-strand	250	1	1
α-helix	266-272	7
α-helix	273-277	5
α-helix	278-296	19
α-helix	318-352	35
α-helix	364-365	2
α-helix	366-370	5
α-helix	371-386	16
α-helix	387-391	5
α-helix	394-407	14

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	53-55	3
α-helix	56-58	3

Chain I: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-39	6	3
α-helix	46-52	7
β-strand	186-188	3	3
β-strand	191	1	4
β-strand	196	1	4
β-strand	197-201	5	3
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-227	7	3
β-strand	234	1	5
β-strand	242	1	5
α-helix	246-255	10
β-strand	264-270	7	3
α-helix	272-281	10
α-helix	284-286	3
α-helix	300-310	11
β-strand	320-323	4	3
α-helix	332-352	21

Chain S: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-12	3	7
β-strand	18-24	7	6
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-51	7	8
β-strand	58-60	3	8
β-strand	69-73	5	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-94	3	7
β-strand	95-99	5	8
β-strand	110-111	2	8
β-strand	115-119	5	7
β-strand	140-141	2	9
β-strand	146-148	3	10
β-strand	155-161	7	9
β-strand	166	1	11
β-strand	172	1	11
β-strand	174-179	6	10
β-strand	186-187	2	10
β-strand	189	1	12
β-strand	195	1	12
β-strand	205-207	3	9
β-strand	211-216	6	9
α-helix	221-223	3
β-strand	226-231	6	10
β-strand	243-246	4	10

Chain T: 6 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-51	5	13
β-strand	58-63	6	14
β-strand	69-74	6	14
β-strand	78-83	6	14
β-strand	88-94	7	14
α-helix	95	1
β-strand	100-105	6	15
β-strand	111-116	6	15
β-strand	121-125	5	15
β-strand	134-139	6	15
β-strand	146-151	6	16
β-strand	156-161	6	16
β-strand	166-170	5	16
β-strand	175-180	6	16
β-strand	187	1	17
β-strand	191-192	2	18
β-strand	198-202	5	18
β-strand	203	1	17
β-strand	207-212	6	18
β-strand	217-223	7	18
β-strand	231-234	4	19
β-strand	240-244	5	19
β-strand	250-254	5	19
β-strand	259-264	6	19
α-helix	272	1
β-strand	273-278	6	20
β-strand	284-289	6	20
β-strand	294-298	5	20
β-strand	304-308	5	20
β-strand	317-320	4	13
β-strand	327-331	5	13
β-strand	335-339	5	13

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	248	synthetic construct
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	T	protein	338	Homo sapiens	P62873 (AlphaFold model)
Relaxin-3 B chain	B	protein	22	Homo sapiens	Q8WXF3
Relaxin-3 A chain	A	protein	24	Homo sapiens	Q8WXF3

Sequence of entity 1 (C), FASTA

>9KFI_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

>9KFI_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 3 (I), FASTA

>9KFI_3 Guanine nucleotide-binding protein G(i) subunit alpha-2 (chains I)
MGCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEDG
YSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPSRADDARQLFALSCTAEEQGVL
PDDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYIPTQQDVLRTRV
KTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEE
MNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGANKYDEA
ASYIQSKFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (S), FASTA

>9KFI_4 scFv16 (chains S)
MVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
AGGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLEL

Sequence of entity 5 (T), FASTA

>9KFI_5 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains T)
ELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMH
WGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICS
IYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTG
HTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFA
TGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKA
DRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 6 (B), FASTA

>9KFI_6 Relaxin-3 B chain (chains B)
GVRLCGREFIRAVIFTCGGSRW

Sequence of entity 7 (A), FASTA

>9KFI_7 Relaxin-3 A chain (chains A)
DVLAGLSSSCCKWGCSKSEISSLC

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:

9KFJ 3.1 Å, Cryo-EM structure of the compound 4-bound human relaxin family peptide receptor 3…

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