7YK7: PDB entry 7YK7

Cryo-EM structure of the DC591053-bound human relaxin family peptide receptor 4 (RXFP4)-Gi complex. Determined by electron microscopy at 2.75 Å resolution. Released 1 Mar 2023.

Method: Electron microscopy
Resolution: 2.75 Å
Organisms: Bos taurus, Homo sapiens, synthetic construct
Chains: 5
Atoms: 8,760
Mol. weight: 154.36 kDa
Ligands: IYM
Released: 1 Mar 2023

Explore 7YK7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YK7 contains 35 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 G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain I: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-40	7	1
α-helix	46-52	7
β-strand	186-191	6	1
β-strand	196-201	6	1
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	276-281	6
α-helix	302-310	9
β-strand	320-324	5	1
α-helix	332-351	20

Chain R: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-63	26
α-helix	75-77	3
α-helix	78-102	25
α-helix	111-144	34
α-helix	155-172	18
α-helix	175-178	4
β-strand	183-184	2	2
β-strand	189-190	2	2
α-helix	200-209	10
α-helix	210-214	5
α-helix	215-232	18
α-helix	238-272	35
α-helix	284-289	6
α-helix	291-298	8
α-helix	301-306	6
α-helix	307-311	5
α-helix	314-321	8

Chain S: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	3
β-strand	12	1	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	69-73	5	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	111	1	5
β-strand	115-117	3	6
β-strand	119	1	4
β-strand	141-142	2	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	195	1	8
β-strand	203-206	4	7
β-strand	211-216	6	7
β-strand	225-231	7	8
β-strand	238-239	2	8
β-strand	243-246	4	8

Chain T: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	38-39	2
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	89-94	6	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	199-203	5	14
β-strand	207-210	4	14
β-strand	221-222	2	14
β-strand	229-234	6	15
β-strand	240-245	6	15
β-strand	250-254	5	15
β-strand	259-264	6	15
β-strand	273-278	6	16
β-strand	284-289	6	16
β-strand	294-298	5	16
β-strand	304-307	4	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

>7YK7_1 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 2 (I), FASTA

>7YK7_2 Guanine nucleotide-binding protein G(i) subunit alpha-2 (chains I)
MGCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEDG
YSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPSRADDARQLFALSCTAEEQGVL
PDDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYIPTQQDVLRTRV
KTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEE
MNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGANKYDEA
ASYIQSKFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (R), FASTA

>7YK7_3 Relaxin-3 receptor 2 (chains R)
MPTLNTSASPPTFFWANASGGSVLSADDAPMPVKFLALRLMVALAYGLVGAIGLLGNLAV
LWVLSNCARRAPGPPSDTFVFNLALADLGLALTLPFWAAESALDFHWPFGGALCKMVLTA
TVLNVYASIFLITALSVARYWVVAMAAGPGTHLSLFWARIATLAVWAAAALVTVPTAVFG
VEGEVCGVRLCLLRFPSRYWLGAYQLQRVVLAFMVPLGVITTSYLLLLAFLQRRQRRRQD
SRVVARSVRILVASFFLCWFPNHVVTLWGVLVKFDLVPWNSTFYTIQTYVFPVTTCLAHS
NSCLNPVLYCLLRREPRQALAGTFRDLRLRLWPQGGGWVQQVALKQVGRRWVASNPRESR
PSTLLTNLDRGTPG

Sequence of entity 4 (S), FASTA

>7YK7_4 scFv16 (chains S)
MVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
AGGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLEL

Sequence of entity 5 (T), FASTA

>7YK7_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
IYM	[(1S)-7-ethoxy-6-methoxy-1-[2-(5-methoxy-1H-indol-3-yl)ethyl]-3,4-dihydro-1H-is…	C28 H35 N3 O5	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

Browse structure collections

About this viewer

MolViewer shows 7YK7 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.