7SK5: ACKR3

Cryo-EM structure of ACKR3 in complex with CXCL12 and an intracellular Fab. Determined by electron microscopy at 4.0 Å resolution. Released 27 Jul 2022.

Method: Electron microscopy
Resolution: 4.0 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 7,232
Mol. weight: 118.12 kDa
Ligands: CLR
Released: 27 Jul 2022

Explore 7SK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SK5 contains 26 α-helices and 66 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: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	1
α-helix	34-38	5
α-helix	41-75	35
β-strand	77-79	3	2
α-helix	81-95	15
α-helix	98-105	8
α-helix	114-147	34
α-helix	154-181	28
β-strand	183-187	5	3
β-strand	194-198	5	3
α-helix	202-204	3
α-helix	205-217	13
α-helix	218-222	5
α-helix	223-241	19
α-helix	243-248	6
α-helix	252-279	28
α-helix	287-312	26
α-helix	313-317	5
α-helix	320-327	8

Chain B: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	15	1	10
β-strand	23	1	1
β-strand	26-31	6	1
β-strand	35-42	8	1
β-strand	47-50	4	1
β-strand	51	1	10
α-helix	56-62	7

Chain E: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	11
β-strand	11-13	3	12
β-strand	20-25	6	11
β-strand	34-39	6	12
β-strand	46-50	5	12
β-strand	54-55	2	12
α-helix	56	1
β-strand	63-66	4	11
β-strand	71-76	6	11
β-strand	86-91	6	12
α-helix	97	1
β-strand	103-106	4	12
β-strand	112	1	13
β-strand	115-119	5	14
α-helix	120-122	3
α-helix	123-127	5
β-strand	130-140	11	14
β-strand	141	1	13
β-strand	146-151	6	15
β-strand	154-156	3	15
β-strand	161-164	4	14
β-strand	174-183	10	14
α-helix	184-189	6
β-strand	193-198	6	15
β-strand	206-210	5	15

Chain F: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	4
β-strand	15	1	5
β-strand	20-28	9	4
β-strand	36-42	7	6
β-strand	48-54	7	6
β-strand	61-63	3	6
α-helix	65-67	3
β-strand	71-76	6	4
α-helix	77-79	3
β-strand	81-87	7	4
β-strand	95-102	8	6
β-strand	111-113	3	2
β-strand	124-126	3	6
β-strand	128	1	5
β-strand	134	1	7
β-strand	137-141	5	8
α-helix	142-144	3
β-strand	154-162	9	8
β-strand	163	1	7
β-strand	168-171	4	9
β-strand	180-182	3	8
α-helix	183-185	3
β-strand	186-187	2	8
β-strand	193-200	8	8
β-strand	211-217	7	9
β-strand	222-228	7	9

Chain K: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	16
β-strand	11	1	17
β-strand	17	1	18
β-strand	20-22	3	16
β-strand	34-39	6	19
β-strand	45-51	7	19
β-strand	58-60	3	19
α-helix	62-64	3
β-strand	68-72	5	16
β-strand	79-83	5	16
β-strand	84	1	18
β-strand	93-99	7	19
β-strand	108-111	4	19
β-strand	115	1	19
β-strand	118	1	17

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
Stromal cell-derived factor 1	B	protein	68	Homo sapiens	P48061 (AlphaFold model)
CID24 Fab light chain	E	protein	215	Homo sapiens
Anti-Fab nanobody	K	protein	123	Lama glama

Sequence of entity 1 (A), FASTA

>7SK5_1 Atypical chemokine receptor 3 (chains A)
GAPDLHLFDYSEPGNFSDISWPCNSSDCIVVDTVMCPNMPNKSVLLYTLSFIYIFIFVIG
MIANSVVVWVNIQAKTTGYDTHCYILNLAIADLWVVLTIPVWVVSLVQHNQWPMGELTCK
VTHLIFSINLFGSIFFLTCMSVDRYLSITYFTNTPSSRKKMVRRVVCILVWLLAFCVSLP
DTYYLKTVTSASNNETYCRSFYPEHSIKEWLIGMELVSVVLGFAVPFSIIAVFYFLLARA
ISASSDQEKHSSRKIIFSYVVVFLVCWLPYHVAVLLDIFSILHYIPFTCRLEHALFTALH
VTQCLSLVHCCVNPVLYSFINRNYRYELMKAFIFKYSAKTGLTKLIDASRVSETEYSALE
QSTKGRPLEVLFQGPHHHHHHHHHHDYKDDDDK

Sequence of entity 2 (F), FASTA

>7SK5_2 CID24 Fab heavy chain (chains F)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNISSSSIHWVRQAPGKGLEWVASISPSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARVSYWDWTWGWSKYEGMDYW
GQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 3 (B), FASTA

>7SK5_3 Stromal cell-derived factor 1 (chains B)
KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQE
YLEKALNK

Sequence of entity 4 (E), FASTA

>7SK5_4 CID24 Fab light chain (chains E)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYYYPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 5 (K), FASTA

>7SK5_5 Anti-Fab nanobody (chains K)
GSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGA
FYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVT
VSS

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	7

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…
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…
7SK6 4.0 Å, Cryo-EM structure of human ACKR3 in complex with chemokine N-terminal mutant CXCL12_LRHQ…

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