7SK4: ACKR3

Cryo-EM structure of ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ, an intracellular Fab, and an extracellular Fab. Determined by electron microscopy at 3.3 Å resolution. Released 27 Jul 2022.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,656
Mol. weight: 152 kDa
Ligands: CLR
Released: 27 Jul 2022

Explore 7SK4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SK4 contains 22 α-helices and 62 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: 15 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	1
β-strand	31-33	3	2
α-helix	35-37	3
α-helix	40-75	36
β-strand	78-79	2	3
α-helix	81-95	15
α-helix	97-105	9
α-helix	114-147	34
α-helix	149-151	3
α-helix	154-181	28
β-strand	183-187	5	4
β-strand	194-198	5	4
α-helix	205-217	13
α-helix	218-222	5
α-helix	223-241	19
α-helix	245-248	4
α-helix	252-279	28
α-helix	287-312	26
α-helix	313-317	5
α-helix	320-330	11

Chain B: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	20-22	3
β-strand	25	1	1
β-strand	28-31	4	2
β-strand	35-38	4	2
β-strand	39	1	5
β-strand	50	1	5
α-helix	56-66	11

Chain C: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	6
β-strand	11-13	3	7
β-strand	20-26	7	6
β-strand	34-39	6	7
β-strand	49-50	2	7
β-strand	54-55	2	7
β-strand	64	1	6
β-strand	67	1	6
β-strand	71-76	6	6
β-strand	86-91	6	7
β-strand	98-99	2	7
β-strand	103-106	4	7

Chain D: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	8
β-strand	14-15	2	9
β-strand	20-28	9	8
α-helix	32-34	3
β-strand	36-42	7	10
β-strand	48-55	8	10
β-strand	61-63	3	10
β-strand	71-76	6	8
β-strand	81-87	7	8
α-helix	91-93	3
β-strand	95-102	8	10
β-strand	105	1	2
β-strand	106	1	11
β-strand	111	1	11
β-strand	117-118	2	10
β-strand	122-124	3	10
β-strand	125-126	2	9

Chain E: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	12
β-strand	20-26	7	12
β-strand	35	1	13
β-strand	36-38	3	14
β-strand	39	1	15
β-strand	46-50	5	14
β-strand	54-55	2	14
α-helix	56	1
β-strand	63-64	2	12
β-strand	71-76	6	12
β-strand	86-87	2	15
β-strand	90-91	2	13
α-helix	97	1
β-strand	98-99	2	13
β-strand	103-104	2	15

Chain F: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	16
β-strand	13-14	2	17
β-strand	20-28	9	16
β-strand	36-42	7	17
β-strand	48-54	7	17
β-strand	62-63	2	17
β-strand	71-76	6	16
β-strand	81-87	7	16
β-strand	95-102	8	17
β-strand	111-112	2	3
β-strand	117-120	4	17
β-strand	124-127	4	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Atypical chemokine receptor 3	A	protein	393	Homo sapiens	P25106 (AlphaFold model)
Stromal cell-derived factor 1	B	protein	69	Homo sapiens	P48061 (AlphaFold model)
CID25 Fab light chain	C	protein	215	Homo sapiens
CID25 Fab heavy chain	D	protein	236	Homo sapiens
CID24 Fab light chain	E	protein	215	Homo sapiens
CID24 Fab heavy chain	F	protein	238	Homo sapiens

Sequence of entity 1 (A), FASTA

>7SK4_1 Atypical chemokine receptor 3 (chains A)
GAPDLHLFDYSEPGNFSDISWPCNSSDCIVVDTVMCPNMPNKSVLLYTLSFIYIFIFVIG
MIANSVVVWVNIQAKTTGYDTHCYILNLAIADLWVVLTIPVWVVSLVQHNQWPMGELTCK
VTHLIFSINLFGSIFFLTCMSVDRYLSITYFTNTPSSRKKMVRRVVCILVWLLAFCVSLP
DTYYLKTVTSASNNETYCRSFYPEHSIKEWLIGMELVSVVLGFAVPFSIIAVFYFLLARA
ISASSDQEKHSSRKIIFSYVVVFLVCWLPYHVAVLLDIFSILHYIPFTCRLEHALFTALH
VTQCLSLVHCCVNPVLYSFINRNYRYELMKAFIFKYSAKTGLTKLIDASRVSETEYSALE
QSTKGRPLEVLFQGPHHHHHHHHHHDYKDDDDK

Sequence of entity 2 (B), FASTA

>7SK4_2 Stromal cell-derived factor 1 (chains B)
LRHQSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQ
EYLEKALNK

Sequence of entity 3 (C), FASTA

>7SK4_3 CID25 Fab light chain (chains C)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYYYPLFTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (D), FASTA

>7SK4_4 CID25 Fab heavy chain (chains D)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNFSYSSIHWVRQAPGKGLEWVAYIYSSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARVYPWWYYKYYHGALDYWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 5 (E), FASTA

>7SK4_5 CID24 Fab light chain (chains E)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYYYPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 6 (F), FASTA

>7SK4_6 CID24 Fab heavy chain (chains F)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNISSSSIHWVRQAPGKGLEWVASISPSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARVSYWDWTWGWSKYEGMDYW
GQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Ligands and cofactors

ID	Name	Formula	Copies
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
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…
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…

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