7SK7: Human ACKR3
Cryo-EM structure of human ACKR3 in complex with CXCL12, a small molecule partial agonist CCX662, and an extracellular Fab. Determined by electron microscopy at 3.3 Å resolution. Released 27 Jul 2022.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organisms
- Homo sapiens, Lama glama
- Chains
- 5
- Atoms
- 6,805
- Mol. weight
- 116.49 kDa
- Ligands
- CLR, GJ9
- Released
- 27 Jul 2022
Explore 7SK7 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7SK7 contains 25 α-helices and 73 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: 12 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 28-33 | 6 | 1 |
| α-helix | 39-70 | 32 | |
| α-helix | 81-95 | 15 | |
| α-helix | 97-105 | 9 | |
| α-helix | 114-147 | 34 | |
| α-helix | 157-181 | 25 | |
| β-strand | 183-187 | 5 | 2 |
| β-strand | 194-198 | 5 | 2 |
| α-helix | 206-217 | 12 | |
| α-helix | 218-222 | 5 | |
| α-helix | 223-235 | 13 | |
| α-helix | 251-279 | 29 | |
| α-helix | 284-285 | 2 | |
| α-helix | 287-312 | 26 | |
| α-helix | 313-317 | 5 | |
Chain B: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-31 | 9 | 1 |
| β-strand | 35-42 | 8 | 1 |
| β-strand | 47-50 | 4 | 1 |
| α-helix | 51-52 | 2 | |
| α-helix | 56-66 | 11 | |
Chain C: 7 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-8 | 3 | 3 |
| β-strand | 11-13 | 3 | 4 |
| β-strand | 20-25 | 6 | 3 |
| β-strand | 34-39 | 6 | 4 |
| β-strand | 47-50 | 4 | 4 |
| β-strand | 54-55 | 2 | 4 |
| α-helix | 56 | 1 | |
| β-strand | 63-66 | 4 | 3 |
| β-strand | 71-76 | 6 | 3 |
| α-helix | 81-83 | 3 | |
| β-strand | 86-91 | 6 | 4 |
| β-strand | 98 | 1 | 4 |
| β-strand | 103-106 | 4 | 4 |
| β-strand | 111 | 1 | 5 |
| β-strand | 112 | 1 | 6 |
| α-helix | 113-114 | 2 | |
| β-strand | 115-119 | 5 | 7 |
| α-helix | 120-122 | 3 | |
| α-helix | 123-128 | 6 | |
| β-strand | 130-140 | 11 | 7 |
| β-strand | 141 | 1 | 6 |
| β-strand | 146-151 | 6 | 8 |
| β-strand | 155-156 | 2 | 8 |
| β-strand | 160-164 | 5 | 7 |
| α-helix | 166-168 | 3 | |
| β-strand | 174-183 | 10 | 7 |
| α-helix | 184-187 | 4 | |
| β-strand | 192-198 | 7 | 8 |
| β-strand | 206-211 | 6 | 8 |
Chain D: 3 helices, 29 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-10 | 5 | 9 |
| β-strand | 15 | 1 | 10 |
| β-strand | 20-23 | 4 | 11 |
| β-strand | 24-28 | 5 | 9 |
| β-strand | 36-42 | 7 | 12 |
| β-strand | 48-55 | 8 | 12 |
| β-strand | 61-63 | 3 | 12 |
| β-strand | 71-76 | 6 | 11 |
| β-strand | 81-87 | 7 | 11 |
| α-helix | 91-93 | 3 | |
| β-strand | 95-102 | 8 | 12 |
| β-strand | 105 | 1 | 1 |
| β-strand | 106 | 1 | 13 |
| β-strand | 111 | 1 | 13 |
| β-strand | 117-118 | 2 | 12 |
| β-strand | 122-124 | 3 | 12 |
| β-strand | 126 | 1 | 10 |
| β-strand | 132 | 1 | 14 |
| β-strand | 135-139 | 5 | 15 |
| β-strand | 152-160 | 9 | 15 |
| β-strand | 161 | 1 | 14 |
| β-strand | 166-169 | 4 | 16 |
| β-strand | 178-180 | 3 | 15 |
| α-helix | 181-183 | 3 | |
| β-strand | 184-185 | 2 | 15 |
| β-strand | 191-198 | 8 | 15 |
| β-strand | 209-210 | 2 | 17 |
| β-strand | 211-214 | 4 | 16 |
| β-strand | 215 | 1 | 18 |
| α-helix | 216-218 | 3 | |
| β-strand | 220 | 1 | 18 |
| β-strand | 225-226 | 2 | 17 |
Chain K: 1 helix, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-7 | 2 | 19 |
| β-strand | 11 | 1 | 20 |
| β-strand | 17 | 1 | 21 |
| β-strand | 20-22 | 3 | 19 |
| β-strand | 33-39 | 7 | 22 |
| β-strand | 45-51 | 7 | 22 |
| β-strand | 58-60 | 3 | 22 |
| β-strand | 61 | 1 | 5 |
| α-helix | 62-64 | 3 | |
| β-strand | 70-72 | 3 | 19 |
| β-strand | 79-81 | 3 | 19 |
| β-strand | 84 | 1 | 21 |
| β-strand | 94 | 1 | 23 |
| β-strand | 95-99 | 5 | 22 |
| β-strand | 110-111 | 2 | 22 |
| β-strand | 115 | 1 | 23 |
| β-strand | 118 | 1 | 20 |
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 | 68 | Homo sapiens | P48061 (AlphaFold model) |
| CID25 Fab light chain | C | protein | 215 | Homo sapiens | |
| CID25 Fab heavy chain | D | protein | 236 | Homo sapiens | |
| Anti-Fab nanobody | K | protein | 123 | Lama glama | |
Sequence of entity 1 (A), FASTA
>7SK7_1 Atypical chemokine receptor 3 (chains A)
GAPDLHLFDYSEPGNFSDISWPCNSSDCIVVDTVMCPNMPNKSVLLYTLSFIYIFIFVIG
MIANSVVVWVNIQAKTTGYDTHCYILNLAIADLWVVLTIPVWVVSLVQHNQWPMGELTCK
VTHLIFSINLFGSIFFLTCMSVDRYLSITYFTNTPSSRKKMVRRVVCILVWLLAFCVSLP
DTYYLKTVTSASNNETYCRSFYPEHSIKEWLIGMELVSVVLGFAVPFSIIAVFYFLLARA
ISASSDQEKHSSRKIIFSYVVVFLVCWLPYHVAVLLDIFSILHYIPFTCRLEHALFTALH
VTQCLSLVHCCVNPVLYSFINRNYRYELMKAFIFKYSAKTGLTKLIDASRVSETEYSALE
QSTKGRPLEVLFQGPHHHHHHHHHHDYKDDDDK
Sequence of entity 2 (B), FASTA
>7SK7_2 Stromal cell-derived factor 1 (chains B)
KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQE
YLEKALNK
Sequence of entity 3 (C), FASTA
>7SK7_3 CID25 Fab light chain (chains C)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYYYPLFTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Sequence of entity 4 (D), FASTA
>7SK7_4 CID25 Fab heavy chain (chains D)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNFSYSSIHWVRQAPGKGLEWVAYIYSSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARVYPWWYYKYYHGALDYWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
Sequence of entity 5 (K), FASTA
>7SK7_5 Anti-Fab nanobody (chains K)
GSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGA
FYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVT
VSS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CLR | Cholesterol | C27 H46 O | 1 |
| GJ9 | (1R)-4-[7-(3-carboxypropoxy)-6-methylquinolin-8-yl]-1-{[2-(4-hydroxypiperidin-1… | C28 H38 N5 O4 S | 1 |
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…
- 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…
Browse structure collections
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