7YK6: PDB entry 7YK6

Cryo-EM structure of the compound 4-bound human relaxin family peptide receptor 4 (RXFP4)-Gi complex. Determined by electron microscopy at 3.03 Å resolution. Released 1 Mar 2023.

Method: Electron microscopy
Resolution: 3.03 Å
Organisms: Bos taurus, Homo sapiens, synthetic construct
Chains: 5
Atoms: 8,736
Mol. weight: 154.25 kDa
Ligands: IYF
Released: 1 Mar 2023

Explore 7YK6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YK6 contains 33 α-helices and 61 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 G: 3 helices, 0 β-strands

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

Chain I: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	33-39	7	1
α-helix	46-52	7
β-strand	186-191	6	1
β-strand	196-201	6	1
α-helix	210-213	4
α-helix	214-216	3
β-strand	221-227	7	1
α-helix	243-255	13
β-strand	264-270	7	1
α-helix	272-281	10
α-helix	284-286	3
α-helix	300-311	12
β-strand	320-324	5	1
α-helix	332-352	21

Chain R: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	40-63	24
α-helix	76-102	27
α-helix	111-140	30
α-helix	141-145	5
α-helix	155-179	25
β-strand	183	1	2
β-strand	190	1	2
α-helix	203-211	9
α-helix	214-232	19
α-helix	238-274	37
α-helix	283-299	17
α-helix	301-306	6
α-helix	307-311	5
α-helix	314-319	6

Chain S: 5 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
α-helix	53-55	3
β-strand	58-60	3	5
α-helix	62-64	3
β-strand	68-73	6	3
α-helix	74-76	3
β-strand	78-84	7	3
α-helix	88-90	3
β-strand	94	1	6
β-strand	95-99	5	5
β-strand	111	1	5
β-strand	115	1	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	203-205	3	7
β-strand	211-216	6	7
β-strand	225-231	7	8
β-strand	244-246	3	8

Chain T: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-34	5
α-helix	38-39	2
α-helix	42-44	3
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	165-170	6	13
β-strand	175-180	6	13
β-strand	187-192	6	14
β-strand	198-203	6	14
β-strand	207-212	6	14
β-strand	220-223	4	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	276-278	3	16
β-strand	284-287	4	16
β-strand	295-298	4	16
β-strand	304	1	16
β-strand	315-320	6	10
β-strand	327-331	5	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	71	Bos taurus	P63212 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-2	I	protein	355	Homo sapiens	P04899 (AlphaFold model)
Relaxin-3 receptor 2	R	protein	374	Homo sapiens	Q8TDU9 (AlphaFold model)
scFv16	S	protein	248	synthetic construct
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	T	protein	345	Homo sapiens	P62873 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>7YK6_1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 2 (I), FASTA

>7YK6_2 Guanine nucleotide-binding protein G(i) subunit alpha-2 (chains I)
MGCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEDG
YSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPSRADDARQLFALSCTAEEQGVL
PDDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYIPTQQDVLRTRV
KTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEE
MNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGANKYDEA
ASYIQSKFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (R), FASTA

>7YK6_3 Relaxin-3 receptor 2 (chains R)
MPTLNTSASPPTFFWANASGGSVLSADDAPMPVKFLALRLMVALAYGLVGAIGLLGNLAV
LWVLSNCARRAPGPPSDTFVFNLALADLGLALTLPFWAAESALDFHWPFGGALCKMVLTA
TVLNVYASIFLITALSVARYWVVAMAAGPGTHLSLFWARIATLAVWAAAALVTVPTAVFG
VEGEVCGVRLCLLRFPSRYWLGAYQLQRVVLAFMVPLGVITTSYLLLLAFLQRRQRRRQD
SRVVARSVRILVASFFLCWFPNHVVTLWGVLVKFDLVPWNSTFYTIQTYVFPVTTCLAHS
NSCLNPVLYCLLRREPRQALAGTFRDLRLRLWPQGGGWVQQVALKQVGRRWVASNPRESR
PSTLLTNLDRGTPG

Sequence of entity 4 (S), FASTA

>7YK6_4 scFv16 (chains S)
MVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
AGGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLEL

Sequence of entity 5 (T), FASTA

>7YK6_5 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains T)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

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

Ligand recognition mechanism of the human relaxin family peptide receptor 4 (RXFP4). Chen, Y., Zhou, Q., Wang, J. et al. Nat Commun (2023) 14:492-492. DOI 10.1038/s41467-023-36182-z · 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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