7YKD: Retinoic acid receptor responder protein 2

Cryo-EM structure of the human chemerin receptor 1 complex with the C-terminal nonapeptide of chemerin. Determined by electron microscopy at 2.81 Å resolution. Released 19 Apr 2023.

Method: Electron microscopy
Resolution: 2.81 Å
Organisms: Homo sapiens, Vicugna pacos
Chains: 6
Atoms: 8,965
Mol. weight: 157.13 kDa
Ligands: CLR
Released: 19 Apr 2023

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

Secondary structure: helices and β-sheets

7YKD contains 36 α-helices and 64 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 A: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-63	29
α-helix	64-68	5
α-helix	73-100	28
α-helix	109-142	34
α-helix	144-150	7
α-helix	153-171	19
α-helix	173-176	4
β-strand	180-183	4	1
β-strand	186-189	4	1
α-helix	211-225	15
α-helix	226-230	5
α-helix	231-249	19
α-helix	257-282	26
α-helix	286-288	3
α-helix	291-316	26
α-helix	320-327	8

Chain B: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	5-24	20
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	89-94	6	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	120-125	6	5
β-strand	134-140	7	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	175-180	6	6
β-strand	187	1	7
β-strand	191-192	2	8
β-strand	198-202	5	8
β-strand	203	1	7
β-strand	207-212	6	8
β-strand	218-223	6	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	260-264	5	9
α-helix	272	1
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	304-308	5	10
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain C: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-40	8	2
α-helix	46-52	7
β-strand	185-191	7	2
β-strand	194-200	7	2
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	2
α-helix	242-254	13
β-strand	263-269	7	2
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-308	13
β-strand	319	1	2
β-strand	322-323	2	2
α-helix	330-351	22

Chain G: 4 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

Chain S: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	11-12	2	12
β-strand	17-23	7	11
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-51	7	13
β-strand	58-60	3	13
β-strand	68-73	6	11
β-strand	78-84	7	11
α-helix	88-90	3
β-strand	92-99	8	13
β-strand	110-111	2	13
β-strand	115-117	3	13
β-strand	118-119	2	12
α-helix	137-139	3
β-strand	140-141	2	14
β-strand	146-148	3	15
β-strand	155-161	7	14
β-strand	166	1	16
β-strand	172	1	16
β-strand	174-179	6	15
β-strand	186-190	5	15
β-strand	194-195	2	15
α-helix	196	1
β-strand	203-208	6	14
β-strand	211-216	6	14
β-strand	225-231	7	15
α-helix	237	1
β-strand	239	1	15
β-strand	243-246	4	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinoic acid receptor responder protein 2	L	protein	9	Homo sapiens	Q99969 (AlphaFold model)
Chemerin-like receptor 1	A	protein	373	Homo sapiens	Q99788 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	C	protein	351	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768
scFV16	S	protein	247	Vicugna pacos

Sequence of entity 1 (L), FASTA

>7YKD_1 Retinoic acid receptor responder protein 2 (chains L)
YFPGQFAFS

Sequence of entity 2 (A), FASTA

>7YKD_2 Chemerin-like receptor 1 (chains A)
MRMEDEDYNTSISYGDEYPDYLDSIVVLEDLSPLEARVTRIFLVVVYSIVCFLGILGNGL
VIIIATFKMKKTVNMVWFLNLAVADFLFNVFLPIHITYAAMDYHWVFGTAMCKISNFLLI
HNMFTSVFLLTIISSDRCISVLLPVWSQNHRSVRLAYMACMVIWVLAFFLSSPSLVFRDT
ANLHGKISCFNNFSLSTPGSSSWPTHSQMDPVGYSRHMVVTVTRFLCGFLVPVLIITACY
LTIVCKLQRNRLAKTKKPFKIIVTIIITFFLCWCPYHTLNLLELHHTAMPGSVFSLGLPL
ATALAIANSCMNPILYVFMGQDFKKFKVALFSRLVNALSEDTGHSSYPSHRSFTKMSSMN
ERTSMNERETGML

Sequence of entity 3 (C), FASTA

>7YKD_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
TLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSE
EECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAEL
AGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTG
IVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRM
HESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYI
QCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (B), FASTA

>7YKD_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (G), FASTA

>7YKD_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 6 (S), FASTA

>7YKD_6 scFV16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	5

Primary citation

Cryo-EM structure of the human chemerin receptor 1-Gi protein complex bound to the C-terminal nonapeptide of chemerin. Wang, J., Chen, G., Liao, Q. et al. Proc Natl Acad Sci U S A (2023) 120:e2214324120-e2214324120. DOI 10.1073/pnas.2214324120 · PubMed

Other PDB entries of the same protein (UniProt Q99969 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JJP 2.9 Å, G protein-coupled receptor 1
8SG1 2.94 Å, Cryo-EM structure of CMKLR1 signaling complex
8ZJG 3.18 Å, Cryo-EM structure of human CMKLR1-Gi complex bound to chemerin
9UYI 3.2 Å, Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and…
8XGM 3.29 Å, Cryo-EM structure of human GPR1 bound to chemerin
9UYH 3.3 Å, Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and…
9UYJ 3.3 Å, Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and…
9UYL 3.3 Å, Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and…
9L3W 3.5 Å, Cryo-EM structure of the chemokine-like receptor 1 in complex with chemerin and Gi1
9UYM 3.5 Å, Composite map of the G protein-coupled receptor 1 (GPR1) bound to chemerin and…
9L3Y 3.6 Å, Cryo-EM structure of the G-protein coupled receptor 1 (GPR1) in complex with chemerin…

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