9L3Z: Inactive chemokine-like receptor 1

Cryo-EM structure of the inactive chemokine-like receptor 1 (CMKLR1). Determined by electron microscopy at 3.9 Å resolution. Released 12 Mar 2025.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Mus musculus, Homo sapiens, Escherichia coli
Chains: 4
Atoms: 5,147
Mol. weight: 107.45 kDa
Released: 12 Mar 2025

Explore 9L3Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L3Z contains 22 α-helices and 44 β-strands across 3 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: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	39-66	28
α-helix	76-90	15
α-helix	115-119	5
α-helix	120-141	22
α-helix	144-147	4
α-helix	155-167	13
α-helix	172-174	3
α-helix	222-225	4
α-helix	226-230	5
α-helix	231-273	43
α-helix	278-297	20
α-helix	299-300	2
α-helix	311-335	25
α-helix	340-352	13
α-helix	353-357	5
α-helix	358-362	5
α-helix	376-392	17
α-helix	413-434	22

Chain H: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	1
β-strand	14-15	2	2
β-strand	21-23	3	3
β-strand	26-28	3	1
β-strand	36-42	7	4
β-strand	48-54	7	4
β-strand	72-73	2	3
β-strand	76	1	5
β-strand	81	1	5
β-strand	84-86	3	3
β-strand	95-102	8	4
α-helix	108-111	4
β-strand	121-123	3	4
β-strand	124-125	2	2
β-strand	136-138	3	6
β-strand	150-157	8	6
β-strand	165-168	4	7
β-strand	177-179	3	6
α-helix	180-182	3
β-strand	183-184	2	6
β-strand	190-198	9	6
β-strand	209-213	5	7
β-strand	214	1	8
β-strand	219	1	8
β-strand	222-224	3	7

Chain L: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	9
β-strand	11-12	2	10
β-strand	20-26	7	9
β-strand	34-39	6	10
β-strand	46-50	5	10
β-strand	63-66	4	9
β-strand	71-76	6	9
β-strand	86-91	6	10
β-strand	100	1	10
β-strand	104-106	3	10
β-strand	116-120	5	11
α-helix	121-123	3
β-strand	134	1	12
β-strand	135-139	5	11
β-strand	141	1	13
β-strand	146-149	4	14
β-strand	164-165	2	11
α-helix	166-169	4
β-strand	175	1	13
β-strand	177-178	2	11
β-strand	181	1	12
β-strand	195-200	6	14
β-strand	207-210	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
The heavy chain of anti-BRIL Fab	H	protein	252	Mus musculus
The light chain of anti-BRIL Fab	L	protein	216	Mus musculus
Chemerin-like receptor 1,Soluble cytochrome b562	A	protein	498	Homo sapiens, Escherichia coli	Q99788 (AlphaFold model)
LRH7-C2	C	protein	7	Homo sapiens

Sequence of entity 1 (H), FASTA

>9L3Z_1 The heavy chain of anti-BRIL Fab (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSGPISTINPCLE
VLFQGPHHHHHH

Sequence of entity 2 (L), FASTA

>9L3Z_2 The light chain of anti-BRIL Fab (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIF
PPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A), FASTA

>9L3Z_3 Chemerin-like receptor 1,Soluble cytochrome b562 (chains A)
MRMEDEDYNTSISYGDEYPDYLDSIVVLEDLSPLEARVTRIFLVVVYSIVCFLGILGNGL
VIIIATFKMKKTVNMVWFLNLAVADFLFNVFLPIHITYAAMDYHWVFGTAMCKISNFLLI
HNMFTSVFLLTIISSDRCISVLLPVWSQNHRSVRLAYMACMVIWVLAFFLSSPSLVFRDT
ANLHGKISCFNNFSLSTPGSSSWPTHSQMDPVGYSRHMVVTVTRFLCGFLVPVLIITACY
LTIVCKLQRNARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATP
PKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKY
LERARSTLTKKPDKIIVTIIITFFLCWCPYHTLNLLELHHTAMPGSVFSLGLPLATALAI
ANSCMNPILYVFMGQDFKKFKVALFSRLVNALEFLEVLFQGPWSHPQFEKGGGSGGGSGG
SAWSHPQFEKDYKDDDDK

Sequence of entity 4 (C), FASTA

>9L3Z_4 LRH7-C2 (chains C)
HWNTVVS

Primary citation

Structural insights into the distinct ligand recognition and signaling of the chemerin receptors CMKLR1 and GPR1. Lin, X., Zhao, L., Cai, H. et al. Protein Cell (2025) 16:381-385. DOI 10.1093/procel/pwae073 · 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…
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
9L3W 3.5 Å, Cryo-EM structure of the chemokine-like receptor 1 in complex with chemerin and Gi1

Browse structure collections

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