8TII: Human ACKR3 phosphorylated by GRK2

Human ACKR3 phosphorylated by GRK2 in complex with Arrestin2 in nanodisc. Determined by electron microscopy at 3.0 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Bos taurus, synthetic construct, Homo sapiens
Chains: 5
Atoms: 6,533
Mol. weight: 154.99 kDa
Released: 22 Jan 2025

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

Secondary structure: helices and β-sheets

8TII contains 15 α-helices and 78 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: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	1
β-strand	19-22	4	1
β-strand	26-28	3	2
β-strand	36-42	7	1
β-strand	53-62	10	3
β-strand	77-87	11	3
α-helix	99-108	10
β-strand	112-118	7	1
β-strand	127-129	3	3
β-strand	141-150	10	3
β-strand	163-168	6	3
β-strand	169-171	3	2
β-strand	183-187	5	4
β-strand	197-203	7	4
β-strand	207	1	5
β-strand	214	1	6
β-strand	216-222	7	4
β-strand	228-240	13	7
β-strand	249-258	10	7
β-strand	262	1	7
β-strand	266-271	6	4
β-strand	274	1	6
β-strand	288-290	3	3
α-helix	291	1
α-helix	299	1
β-strand	300	1	3
α-helix	301-303	3
β-strand	318-329	12	7
β-strand	343-349	7	7
β-strand	350	1	5

Chain H: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	8
β-strand	20-28	9	8
α-helix	32-34	3
β-strand	35-42	8	9
β-strand	48-55	8	9
β-strand	60-63	4	9
β-strand	68	1	8
β-strand	71-76	6	8
β-strand	81-87	7	8
α-helix	91-93	3
β-strand	95-103	9	9
β-strand	121-122	2	9
β-strand	126-128	3	9
β-strand	136	1	10
β-strand	139-143	5	11
β-strand	155-164	10	11
β-strand	165	1	10
β-strand	170-173	4	12
β-strand	183-184	2	11
α-helix	185-187	3
β-strand	188-189	2	11
β-strand	195-203	9	11
β-strand	213-219	7	12
α-helix	220-222	3
β-strand	224-230	7	12

Chain L: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	13
β-strand	11-14	4	14
β-strand	21-26	6	13
β-strand	34-39	6	14
β-strand	46-50	5	14
β-strand	54-55	2	14
α-helix	56	1
β-strand	63-67	5	13
β-strand	71-76	6	13
β-strand	86-91	6	14
β-strand	98-99	2	14
β-strand	104-107	4	14
α-helix	113-114	2
β-strand	115-119	5	15
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	15
β-strand	145-150	6	16
β-strand	160-161	2	15
β-strand	164-165	2	15
α-helix	166	1
β-strand	174-183	10	15
α-helix	184-187	4
β-strand	192-199	8	16
β-strand	206-211	6	16

Chain N: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	17
β-strand	17-23	7	17
β-strand	35-40	6	18
β-strand	43-51	9	18
β-strand	58-60	3	18
α-helix	62-64	3
β-strand	68-73	6	17
β-strand	78-84	7	17
β-strand	92-97	6	18
β-strand	99	1	19
β-strand	108	1	19
β-strand	115-117	3	18

Chain R: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	353-356	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-arrestin-1	A	protein	418	Bos taurus	P17870 (AlphaFold model)
Fab7 heavy chain	H	protein	240	synthetic construct
Fab7 light chain	L	protein	215	synthetic construct
anti-Fab nanobody	N	protein	123	synthetic construct
Atypical chemokine receptor 3	R	protein	393	Homo sapiens	P25106 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8TII_1 Beta-arrestin-1 (chains A)
MGDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVEPVDGVVLVDPEYLKERRVYVTLTCA
FRYGREDLDVLGLTFRKDLFVANVQSFPPAPEDKKPLTRLQERLIKKLGEHAYPFTFEIP
PNLPCSVTLQPGPEDTGKACGVDYEVKAFCAENLEEKIHKRNSVRLVIRKVQYAPERPGP
QPTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYAD
ICLFNTAQYKCPVAMEEADDTVAPSSTFCKVYTLTPFLANNREKRGLALDGKLKHEDTNL
ASSTLLREGANREILGIIVSYKVKVKLVVSRGGLLGDLASSDVAVELPFTLMHPKPKEEP
PHREVPEHETPVDTNLIELDTNDDDAAAEDFARQRLKGMKDDKEEEEDGTGSPRLNDR

Sequence of entity 2 (H), FASTA

>8TII_2 Fab7 heavy chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVSSSYIHWVRQAPGKGLEWVASISSYYGY
TYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARKSMYHRGWGWLSWVYGAMD
YWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (L), FASTA

>8TII_3 Fab7 light chain (chains L)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYYYPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (N), FASTA

>8TII_4 anti-Fab nanobody (chains N)
GSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGA
FYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVT
VSS

Sequence of entity 5 (R), FASTA

>8TII_5 Atypical chemokine receptor 3 (chains R)
GAPDLHLFDYSEPGNFSDISWPCNSSDCIVVDTVMCPNMPNKSVLLYTLSFIYIFIFVIG
MIANSVVVWVNIQAKTTGYDTHCYILNLAIADLWVVLTIPVWVVSLVQHNQWPMGELTCK
VTHLIFSINLFGSIFFLTCMSVDRYLSITYFTNTPSSRKKMVRRVVCILVWLLAFCVSLP
DTYYLKTVTSASNNETYCRSFYPEHSIKEWLIGMELVSVVLGFAVPFSIIAVFYFLLARA
ISASSDQEKHSSRKIIFSYVVVFLVCWLPYHVAVLLDIFSILHYIPFTCRLEHALFTALH
VTQCLSLVHCCVNPVLYSFINRNYRYELMKAFIFKYSAKTGLTKLIDASRVSETEYSALE
QSTKGRPLEVLFQGPHHHHHHHHHHDYKDDDDK

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 P17870 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1G4M 1.9 Å, Crystal structure of bovine beta-arrestin 1
1G4R 2.2 Å, Crystal structure of bovine beta-arrestin 1
3GC3 2.2 Å, Crystal Structure of Arrestin2S and Clathrin
7DFC 2.49 Å, Crystal of Arrestin2-V2Rpp-3-Fab30 complex
7DFA 2.54 Å, Crystal of Arrestin2-V2Rpp-4-Fab30 complex
22GM 2.7 Å, C5a bound C5aR1 in complex with beta-arrestin1
9WSV 2.8 Å, Cryo-EM structure of DAMGO-muOR-arrestin-1-Fab30 complex
9WSX 2.8 Å, Cryo-EM structure of endomorphin-1-muOR-arrestin2-Fab30 complex
22GK 2.84 Å, C5a bound C5aR2 in complex with beta-arrestin1
1JSY 2.9 Å, Crystal structure of bovine arrestin-2
1ZSH 2.9 Å, Crystal structure of bovine arrestin-2 in complex with inositol hexakisphosphate (IP6)
22CR 2.9 Å, C5a-desArg bound C5aR2 in complex with beta-arrestin1

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