7SK9: Human ACKR3

Cryo-EM structure of human ACKR3 in complex with a small molecule partial agonist CCX662, and an intracellular Fab. Determined by electron microscopy at 3.7 Å resolution. Released 27 Jul 2022.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,700
Mol. weight: 95.36 kDa
Ligands: GJ9, CLR
Released: 27 Jul 2022

Explore 7SK9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SK9 contains 24 α-helices and 52 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: 15 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	41-72	32
α-helix	73-75	3
β-strand	77-79	3	1
α-helix	81-105	25
α-helix	114-147	34
α-helix	149-151	3
α-helix	154-181	28
β-strand	183-185	3	2
β-strand	196-198	3	2
α-helix	205-217	13
α-helix	218-222	5
α-helix	223-241	19
α-helix	244-248	5
α-helix	254-279	26
α-helix	287-304	18
α-helix	306-309	4
α-helix	311-315	5
α-helix	320-328	9

Chain E: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	9
β-strand	11-13	3	10
β-strand	20-25	6	9
β-strand	34-38	5	11
β-strand	39	1	12
β-strand	46-50	5	11
β-strand	54-55	2	11
β-strand	57	1	13
β-strand	59	1	13
β-strand	63-68	6	9
β-strand	71-76	6	9
α-helix	81-83	3
β-strand	86	1	12
β-strand	89-91	3	11
α-helix	97	1
β-strand	98	1	11
β-strand	104-106	3	10
β-strand	112	1	14
α-helix	113-114	2
β-strand	115-119	5	15
α-helix	123-128	6
β-strand	130-140	11	15
β-strand	141	1	14
β-strand	146-151	6	16
β-strand	154-156	3	16
β-strand	161-164	4	15
β-strand	174-183	10	15
α-helix	184-189	6
β-strand	192-198	7	16
β-strand	206-211	6	16

Chain F: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	3
β-strand	15	1	4
β-strand	20-26	7	3
α-helix	32-34	3
β-strand	36-42	7	5
β-strand	48-54	7	5
β-strand	62-63	2	5
α-helix	65-67	3
β-strand	71-76	6	3
β-strand	81-87	7	3
α-helix	91-93	3
β-strand	95-102	8	5
β-strand	111-113	3	1
β-strand	119-120	2	5
β-strand	125-126	2	5
β-strand	128	1	4
β-strand	134	1	6
β-strand	137-141	5	7
β-strand	152-162	11	7
β-strand	163	1	6
β-strand	168-171	4	8
β-strand	176	1	8
β-strand	180-182	3	7
α-helix	183-185	3
β-strand	186-187	2	7
β-strand	193-202	10	7
β-strand	211-217	7	8
β-strand	222-228	7	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Atypical chemokine receptor 3	A	protein	393	Homo sapiens	P25106 (AlphaFold model)
CID24 Fab heavy chain	F	protein	238	Homo sapiens
CID24 Fab light chain	E	protein	215	Homo sapiens

Sequence of entity 1 (A), FASTA

>7SK9_1 Atypical chemokine receptor 3 (chains A)
GAPDLHLFDYSEPGNFSDISWPCNSSDCIVVDTVMCPNMPNKSVLLYTLSFIYIFIFVIG
MIANSVVVWVNIQAKTTGYDTHCYILNLAIADLWVVLTIPVWVVSLVQHNQWPMGELTCK
VTHLIFSINLFGSIFFLTCMSVDRYLSITYFTNTPSSRKKMVRRVVCILVWLLAFCVSLP
DTYYLKTVTSASNNETYCRSFYPEHSIKEWLIGMELVSVVLGFAVPFSIIAVFYFLLARA
ISASSDQEKHSSRKIIFSYVVVFLVCWLPYHVAVLLDIFSILHYIPFTCRLEHALFTALH
VTQCLSLVHCCVNPVLYSFINRNYRYELMKAFIFKYSAKTGLTKLIDASRVSETEYSALE
QSTKGRPLEVLFQGPHHHHHHHHHHDYKDDDDK

Sequence of entity 2 (F), FASTA

>7SK9_2 CID24 Fab heavy chain (chains F)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNISSSSIHWVRQAPGKGLEWVASISPSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARVSYWDWTWGWSKYEGMDYW
GQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (E), FASTA

>7SK9_3 CID24 Fab light chain (chains E)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYYYPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
GJ9	(1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1…	C28 H38 N5 O4 S	1
CLR	Cholesterol	C27 H46 O	2

Primary citation

Structures of atypical chemokine receptor 3 reveal the basis for its promiscuity and signaling bias. Yen, Y.C., Schafer, C.T., Gustavsson, M. et al. Sci Adv (2022) 8:eabn8063-eabn8063. DOI 10.1126/sciadv.abn8063 · PubMed

Other PDB entries of the same protein (UniProt P25106 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6K3F 2.3 Å, Crystal Structure of beta-Arrestin 2 in Complex with CXCR7 Phosphopeptide
8TII 3.0 Å, Human ACKR3 phosphorylated by GRK2 in complex with Arrestin2 in nanodisc
7SK4 3.3 Å, Cryo-EM structure of ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ, an…
7SK7 3.3 Å, Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial…
7SK8 3.3 Å, Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial…
8VJ9 3.3 Å, CryoEM structure of human ACKR3 phosphorylated by GRK5 in complex with Arrestin3 variant…
9E82 3.4 Å, ACKR3 phosphorylated by GRK5 in complex with arrestin2 and Fab7
8TIO 3.6 Å, Human ACKR3 with C tail extended by 12 glycines phosphorylated by GRK5 in complex with…
7SK3 3.8 Å, Cryo-EM structure of ACKR3 in complex with CXCL12, an intracellular Fab, and an…
8TIL 3.8 Å, Human ACKR3 phosphorylated by GRK5 in complex with Arrestin3 reconstructed without…
7SK5 4.0 Å, Cryo-EM structure of ACKR3 in complex with CXCL12 and an intracellular Fab
7SK6 4.0 Å, Cryo-EM structure of human ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ…

Browse structure collections

About this viewer

MolViewer shows 7SK9 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.