8YNF: Atypical chemokine receptor 1

Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8. Determined by electron microscopy at 3.65 Å resolution. Released 17 Sept 2025.

Method: Electron microscopy
Resolution: 3.65 Å
Organism: Homo sapiens
Chains: 6
Atoms: 4,636
Mol. weight: 119.55 kDa
Released: 17 Sept 2025

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

Secondary structure: helices and β-sheets

8YNF contains 28 α-helices and 14 β-strands across 6 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: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	66-80	15
α-helix	96-116	21
α-helix	126-152	27
α-helix	164-180	17
α-helix	182-186	5
β-strand	188-191	4	3
β-strand	194-197	4	3
α-helix	201-203	3
α-helix	204-215	12
α-helix	216-220	5
α-helix	221-226	6
α-helix	247-267	21
α-helix	276-294	19
α-helix	296-310	15

Chain B: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	66-81	16
α-helix	96-116	21
α-helix	126-152	27
α-helix	164-180	17
α-helix	182-186	5
β-strand	188-191	4	1
β-strand	194-197	4	1
α-helix	201-203	3
α-helix	204-215	12
α-helix	216-220	5
α-helix	221-226	6
α-helix	247-267	21
α-helix	276-294	19
α-helix	296-310	15

Chain D: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	24-28	5	2
β-strand	39-42	4	2
β-strand	49-51	3	2
α-helix	62-67	6

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	2
β-strand	42	1	2
α-helix	63-67	5

Chain G: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	4
β-strand	41-42	2	4
α-helix	63-67	5

Chain H: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	24-28	5	4
β-strand	39-42	4	4
β-strand	49-51	3	4
α-helix	59-67	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Atypical chemokine receptor 1	A, B	protein	392	Homo sapiens	Q16570 (AlphaFold model)
IL-8(9-77)	D, E, G, H	protein	79	Homo sapiens	P10145 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8YNF_1 Atypical chemokine receptor 1 (chains A, B)
MGKTIIALSYIFCLVFADYKDDDYAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSGNC
LHRAELSPSTENSSQLDFEDVWNSSYGVNDSFPDGDYGANLEAAAPCHSCNLLDDSALPF
FILTSVLGILASSTVLFMLFRPLFRWQLCPGWPVLAQLAVGSALFSIVVPVLAPGLGSTR
SSALCSLGYCVWYGSAFAQALLLGCHASLGHRLGAGQVPGLTLGLTVGIWGVAALLTLPV
TLASGASGGLCTLIYSTELKALQATHTVACLAIFVLLPLGLFGAKGLKKALGMGPGPWMN
ILWAWFIFWWPHGVVLGLDFLVRSKLLLLSTCLAQQALDLLLNLAEALAILHCVATPLLL
ALFCHQATRTLLPSLPLPEGWSSHLDTLGSKS

Sequence of entity 2 (D, E, G, H), FASTA

>8YNF_2 IL-8(9-77) (chains D, E, G, H)
EGAVLPRSAKELRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDP
KENWVQRVVEKFLKRAENS

Primary citation

Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8. Banerjee, R., Khanppnavar, B., Maharana, J. et al. To be published.

Other PDB entries of the same protein (UniProt Q16570 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P93 1.55 Å, Crystal Structure of leukotoxin LukE from Staphylococcus aureus in complex with a…
4NUU 1.95 Å, Heterotrimer structure of Region II from Plasmodium vivax Duffy Binding Protein (PvDBP)…
8A44 2.49 Å, Plasmodium vivax Duffy binding protein region II bound the DARC ectodomain and…
4NUV 2.6 Å, Heterotetramer structure of Region II from Plasmodium vivax Duffy Binding Protein…
8JPS 3.65 Å, Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the…

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