8SG1: CMKLR1 signaling complex

Cryo-EM structure of CMKLR1 signaling complex. Determined by electron microscopy at 2.94 Å resolution. Released 1 Nov 2023.

Method: Electron microscopy
Resolution: 2.94 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,846
Mol. weight: 146.76 kDa
Ligands: PLM, CLR
Released: 1 Nov 2023

Explore 8SG1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SG1 contains 37 α-helices and 63 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
α-helix	30-32	3
β-strand	33-40	8	9
α-helix	46-53	8
β-strand	185-190	6	9
β-strand	195-200	6	9
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	9
α-helix	227-229	3
α-helix	242-254	13
β-strand	263-269	7	9
α-helix	271-278	8
α-helix	296-308	13
β-strand	319-323	5	9
α-helix	331-351	21

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	9-24	16
α-helix	30-33	4
α-helix	38-43	6
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	120-125	6	4
β-strand	134-140	7	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	175-181	7	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	220-223	4	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-264	6	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain E: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	17-24	8	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	65	1	10
β-strand	68-73	6	10
β-strand	78-84	7	10
β-strand	92-99	8	11
β-strand	111	1	11
β-strand	115-117	3	11
β-strand	141-142	2	12
β-strand	147	1	13
β-strand	156-162	7	12
β-strand	167	1	14
β-strand	173	1	14
β-strand	175	1	15
β-strand	177-180	4	13
β-strand	186-191	6	13
β-strand	195-196	2	13
α-helix	197	1
β-strand	204-208	5	12
β-strand	212-217	6	12
α-helix	222-224	3
β-strand	226-229	4	13
β-strand	231	1	16
β-strand	232	1	15
β-strand	240	1	16
β-strand	244-246	3	13

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	11-20	10
α-helix	30-43	14
α-helix	53-55	3

Chain R: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	37-64	28
α-helix	74-91	18
α-helix	93-100	8
α-helix	109-111	3
α-helix	115-125	11
α-helix	128-142	15
α-helix	144-149	6
α-helix	153-171	19
α-helix	173-177	5
β-strand	178-183	6	1
β-strand	186-191	6	1
α-helix	215-225	11
α-helix	226-230	5
α-helix	231-250	20
α-helix	257-282	26
α-helix	283-285	3
α-helix	292-306	15
α-helix	308-311	4
α-helix	313-317	5
α-helix	321-326	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chemerin-like receptor 1	R	protein	292	Homo sapiens	Q99788 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	336	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	54	Homo sapiens	P59768 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	351	Homo sapiens	P63096 (AlphaFold model)
Chemerin 9	L	protein	9	Homo sapiens	Q99969
scFv16	E	protein	266	Mus musculus

Sequence of entity 1 (R), FASTA

>8SG1_1 Chemerin-like receptor 1 (chains R)
ARVTRIFLVVVYSIVCFLGILGNGLVIIIATFKMKKTVNMVWFLNLAVADFLFNVFLPIH
ITYAAMDYHWVFGTAMCKISNFLLIHNMFTSVFLLTIISSDRCISVLLPVWSQNHRSVRL
AYMACMVIWVLAFFLSSPSLVFRDTANLHGKISCFNNFSLSTPGSSSWPTHSQMDPVGYS
RHMVVTVTRFLCGFLVPVLIITACYLTIVCKLQRNRLAKTKKPFKIIVTIIITFFLCWCP
YHTLNLLELHHTAMPGSVFSLGLPLATALAIANSCMNPILYVFMGQDFKKFK

Sequence of entity 2 (B), FASTA

>8SG1_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
DQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWG
TDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIY
NLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHT
GDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATG
SDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADR
AGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>8SG1_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
IAQARKLVQQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASQNPFR

Sequence of entity 4 (A), FASTA

>8SG1_4 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
TLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAGYSE
EECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAEL
AGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTG
IVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRM
HASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYI
QCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 5 (L), FASTA

>8SG1_5 Chemerin 9 (chains L)
YFPGQFAFS

Sequence of entity 6 (E), FASTA

>8SG1_6 scFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELLEENLYFQGASHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	2
CLR	Cholesterol	C27 H46 O	1

Primary citation

Structural basis of G protein-Coupled receptor CMKLR1 activation and signaling induced by a chemerin-derived agonist. Zhang, X., Weiss, T., Cheng, M.H. et al. PLoS Biol (2023) 21:e3002188-e3002188. DOI 10.1371/journal.pbio.3002188 · PubMed

Other PDB entries of the same protein (UniProt Q99788 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7YKD 2.81 Å, Cryo-EM structure of the human chemerin receptor 1 complex with the C-terminal…
8ZJG 3.18 Å, Cryo-EM structure of human CMKLR1-Gi complex bound to chemerin
9L3W 3.5 Å, Cryo-EM structure of the chemokine-like receptor 1 in complex with chemerin and Gi1
9L3Z 3.9 Å, Cryo-EM structure of the inactive chemokine-like receptor 1 (CMKLR1)

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