9KFK: PDB entry 9KFK

Cryo-EM structure of the relaxin-3-bound human relaxin family peptide receptor 4 (RXFP4)-Gi complex. Determined by electron microscopy at 2.95 Å resolution. Released 13 Aug 2025.

Method: Electron microscopy
Resolution: 2.95 Å
Organisms: Bos taurus, Homo sapiens, Escherichia coli
Chains: 7
Atoms: 9,039
Mol. weight: 189.45 kDa
Released: 13 Aug 2025

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

Secondary structure: helices and β-sheets

9KFK contains 40 α-helices and 63 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: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	17-21	5

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-21	11

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-42	13
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	33-39	7	1
α-helix	46-52	7
β-strand	186-192	7	1
β-strand	195-201	7	1
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-227	7	1
α-helix	228-230	3
α-helix	243-255	13
β-strand	264-270	7	1
α-helix	272-281	10
α-helix	284-286	3
α-helix	298-309	12
β-strand	320-324	5	1
α-helix	332-351	20

Chain R: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-63	28
α-helix	75-77	3
α-helix	78-91	14
α-helix	94-102	9
α-helix	111-114	4
α-helix	120-140	21
α-helix	141-145	5
α-helix	155-177	23
β-strand	183-185	3	2
β-strand	188-190	3	2
α-helix	197-201	5
α-helix	202-209	8
α-helix	210-214	5
α-helix	215-233	19
α-helix	241-274	34
α-helix	285-299	15
α-helix	301-309	9
α-helix	314-324	11

Chain S: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	3
β-strand	11-12	2	4
β-strand	17-23	7	3
α-helix	29-31	3
β-strand	33-39	7	5
β-strand	45-51	7	5
α-helix	53-55	3
β-strand	58-60	3	5
β-strand	69-73	5	3
α-helix	74-76	3
β-strand	78-84	7	3
α-helix	88-90	3
β-strand	92-94	3	6
β-strand	95-99	5	5
β-strand	110-111	2	5
β-strand	115-117	3	6
β-strand	118-119	2	4
β-strand	140-141	2	7
β-strand	146-148	3	8
β-strand	155-161	7	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	195	1	8
β-strand	203-206	4	7
β-strand	211-216	6	7
β-strand	225-231	7	8
β-strand	243-246	4	8

Chain T: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-52	6	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	166-170	5	13
β-strand	175-180	6	13
β-strand	187	1	14
β-strand	191-192	2	15
β-strand	198-202	5	15
β-strand	203	1	14
β-strand	207-212	6	15
β-strand	218-223	6	15
β-strand	229-234	6	16
β-strand	240-245	6	16
β-strand	249-254	6	16
β-strand	259-264	6	16
β-strand	273-278	6	17
β-strand	284-289	6	17
β-strand	294-298	5	17
β-strand	303-308	6	17
β-strand	319-320	2	10
β-strand	327-330	4	10
β-strand	335-339	5	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	55	Bos taurus	P63212 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-2	I	protein	355	Homo sapiens	P04899 (AlphaFold model)
Soluble cytochrome b562,Relaxin-3 receptor 2,LgBiT	R	protein	678	Escherichia coli, Homo sapiens, synthetic construct	Q8TDU9 (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	19	Homo sapiens	Q8WXF3
Relaxin-3 A chain	A	protein	24	Homo sapiens	Q8WXF3

Sequence of entity 1 (G), FASTA

>9KFK_1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 2 (I), FASTA

>9KFK_2 Guanine nucleotide-binding protein G(i) subunit alpha-2 (chains I)
MGCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEDG
YSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPSRADDARQLFALSCTAEEQGVL
PDDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYIPTQQDVLRTRV
KTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEE
MNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGANKYDEA
ASYIQSKFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (R), FASTA

>9KFK_3 Soluble cytochrome b562,Relaxin-3 receptor 2,LgBiT (chains R)
MKTIIALSYIFCLVFAHHHHHHHHHHADLEDNWETLNDNLKVIEKADNAAQVKDALTKMR
AAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQL
KTTRNAYIQKYLPTLNTSASPPTFFWANASGGSVLSADDAPMPVKFLALRLMVALAYGLV
GAIGLLGNLAVLWVLSNCARRAPGPPSDTFVFNLALADLGLALTLPFWAAESALDFHWPF
GGALCKMVLTATVLNVYASIFLITALSVARYWVVAMAAGPGTHLSLFWARIATLAVWAAA
ALVTVPTAVFGVEGEVCGVRLCLLRFPSRYWLGAYQLQRVVLAFMVPLGVITTSYLLLLA
FLQRRQRRRQDSRVVARSVRILVASFFLCWFPNHVVTLWGVLVKFDLVPWNSTFYTIQTY
VFPVTTCLAHSNSCLNPVLYCLLRREPRQALAGTFRDLRLRLWPQGGGWVQQVALKQVGR
RWVASNPRESRPSTLLTNLDRGTPGGSSGGGGSGGGGSSGVFTLEDFVGDWEQTAAYNLD
QVLEQGGVSSLLQNLAVSVTPIQRIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKV
VYPVDDHHFKVILPYGTLVIDGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIID
ERLITPDGSMLFRVTINS

Sequence of entity 4 (S), FASTA

>9KFK_4 scFv16 (chains S)
MVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
AGGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLEL

Sequence of entity 5 (T), FASTA

>9KFK_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

>9KFK_6 Relaxin-3 B chain (chains B)
LCGREFIRAVIFTCGGSRW

Sequence of entity 7 (A), FASTA

>9KFK_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 P63212 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3V5W 2.07 Å, Human G Protein-Coupled Receptor Kinase 2 in Complex with Soluble Gbetagamma Subunits…
1GP2 2.3 Å, G protein heterotrimer GI_ALPHA_1 BETA_1 GAMMA_2 with GDP bound
5WG4 2.31 Å, Human GRK2 in complex with Gbetagamma subunits and CCG257284
9IJE 2.34 Å, Epinephrine-activated human beta3 adrenergic receptor
1GG2 2.4 Å, G protein heterotrimer mutant GI_ALPHA_1(G203A) BETA_1 GAMMA_2 with GDP bound
4MK0 2.4 Å, Crystal structure of G protein-coupled receptor kinase 2 in complex with a a rationally…
8YK0 2.4 Å, Cryo-EM structure of human GPR156-Gi3 complex
8Z9O 2.4 Å, Cryo-EM structure of human GPR4-Gs complex
22ES 2.43 Å, Gi bound kappa-opioid receptor in complex with difelikefalin
6U7C 2.44 Å, Human GRK2 in complex with Gbetagamma subunits and CCG258747
9WG6 2.44 Å, D1R-Gs in complexed with Dopamine/LY3154207/BMSA1/UNC9815
8JIS 2.46 Å, Cryo-EM structure of the GLP-1R/GCGR dual agonist peptide15-bound human GLP-1R-Gs complex

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