8VJ9: Human ACKR3 phosphorylated by GRK5

CryoEM structure of human ACKR3 phosphorylated by GRK5 in complex with Arrestin3 variant with the C edge loop from Arrestin2 inserted. Determined by electron microscopy at 3.3 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: synthetic construct, Homo sapiens, Bos taurus
Chains: 4
Atoms: 5,511
Mol. weight: 139.41 kDa
Released: 22 Jan 2025

Explore 8VJ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VJ9 contains 11 α-helices and 68 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: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	13
β-strand	19-23	5	13
β-strand	28-29	2	14
β-strand	30	1	15
β-strand	35	1	15
β-strand	38-44	7	13
α-helix	46-49	4
β-strand	53-63	11	16
β-strand	77	1	16
β-strand	84-88	5	16
α-helix	100-107	8
β-strand	113-118	6	13
β-strand	128-131	4	16
β-strand	142-152	11	16
β-strand	165-167	3	16
β-strand	171-172	2	14
β-strand	184-188	5	17
β-strand	198-204	7	17
β-strand	208	1	18
β-strand	215-223	9	17
α-helix	227-229	3
β-strand	231-242	12	19
β-strand	253-259	7	19
β-strand	267-275	9	17
β-strand	288-291	4	16
β-strand	301	1	16
β-strand	318-329	12	19
β-strand	337-342	6	19
β-strand	343	1	18
α-helix	346-348	3

Chain H: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	19-28	10	1
β-strand	35-42	8	2
β-strand	49-55	7	2
β-strand	60-63	4	2
α-helix	65-67	3
β-strand	68	1	1
β-strand	71-76	6	1
β-strand	81-89	9	1
α-helix	91-93	3
β-strand	95-103	9	2
β-strand	121-122	2	2
β-strand	126-128	3	2
β-strand	136	1	3
β-strand	139-143	5	4
β-strand	155-164	10	4
β-strand	165	1	3
β-strand	172-173	2	5
β-strand	183-189	7	4
β-strand	195-203	9	4
α-helix	205-207	3
β-strand	213-219	7	5
β-strand	224-230	7	5

Chain L: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	6
β-strand	11-12	2	7
β-strand	20-26	7	6
β-strand	35-39	5	8
β-strand	47	1	8
β-strand	49-50	2	9
β-strand	54-55	2	9
β-strand	63-67	5	6
β-strand	71-76	6	6
β-strand	86-91	6	8
β-strand	98-99	2	8
β-strand	104-105	2	7
β-strand	112	1	10
β-strand	115-119	5	11
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	11
β-strand	141	1	10
β-strand	145-150	6	12
β-strand	160-161	2	11
β-strand	164	1	11
α-helix	166-168	3
β-strand	174-183	10	11
α-helix	184-189	6
β-strand	192-199	8	12
β-strand	206-211	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab7 heavy chain	H	protein	240	synthetic construct
Fab7 light chain	L	protein	215	synthetic construct
Atypical chemokine receptor 3	R	protein	393	Homo sapiens	P25106 (AlphaFold model)
Beta-arrestin-2	A	protein	400	Bos taurus	P32120 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>8VJ9_1 Fab7 heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVSSSYIHWVRQAPGKGLEWVASISSYYGY
TYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARKSMYHRGWGWLSWVYGAMD
YWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (L), FASTA

>8VJ9_2 Fab7 light chain (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYYYPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (R), FASTA

>8VJ9_3 Atypical chemokine receptor 3 (chains R)
GAPDLHLFDYSEPGNFSDISWPCNSSDCIVVDTVMCPNMPNKSVLLYTLSFIYIFIFVIG
MIANSVVVWVNIQAKTTGYDTHCYILNLAIADLWVVLTIPVWVVSLVQHNQWPMGELTCK
VTHLIFSINLFGSIFFLTCMSVDRYLSITYFTNTPSSRKKMVRRVVCILVWLLAFCVSLP
DTYYLKTVTSASNNETYCRSFYPEHSIKEWLIGMELVSVVLGFAVPFSIIAVFYFLLARA
ISASSDQEKHSSRKIIFSYVVVFLVCWLPYHVAVLLDIFSILHYIPFTCRLEHALFTALH
VTQCLSLVHCCVNPVLYSFINRNYRYELMKAFIFKYSAKTGLTKLIDASRVSETEYSALE
QSTKGRPLEVLFQGPHHHHHHHHHHDYKDDDDK

Sequence of entity 4 (A), FASTA

>8VJ9_4 Beta-arrestin-2 (chains A)
MGEKPGTRVFKKSSPNCKLTVYLGKRDFVDHLDKVDPVDGVVLVDPDYLKDRKVFVTLTC
AFRYGREDLDVLGLSFRKDLFIANYQAFPPTPNPPRPPTRLQERLLRKLGQHAHPFFFTI
PQNLPCSVTLQPGPEDTGKACGVDFEIRAFCAKSLEEKSHKRNSVRLVIRKVQFAPEKPG
PQPSAETTRHFLMSDRSLHLEASLDKELYYHGEPLNVNVHVTNNSTKTVKKIKVSVRQYA
DICLFSTAQYKCPVAQVEQDDQVSPSSTFCKVYTITPLLSNNREKRGLALDGKLKHEDTN
LASSTIVKEGANKEVLGILVSYRVKVKLVVSRGGLLGDLASSDVSVELPFVLMHPKPHDH
IALPRPQSAVPETDAPVDTNLIEFETNYATDDDIVFEDFA

Primary citation

Effect of phosphorylation barcodes on arrestin binding to a chemokine receptor. Chen, Q., Schafer, C.T., Mukherjee, S. et al. Nature (2025) 643:280-287. DOI 10.1038/s41586-025-09024-9 · 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…
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…
7SK9 3.7 Å, Cryo-EM structure of human ACKR3 in complex with a small molecule partial agonist…
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

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