7SK3: ACKR3
Cryo-EM structure of ACKR3 in complex with CXCL12, an intracellular Fab, and an extracellular Fab. Determined by electron microscopy at 3.8 Å resolution. Released 27 Jul 2022.
- Method
- Electron microscopy
- Resolution
- 3.8 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 6,803
- Mol. weight
- 154.11 kDa
- Ligands
- CLR
- Released
- 27 Jul 2022
Explore 7SK3 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7SK3 contains 25 α-helices and 57 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: 17 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-33 | 3 | 1 |
| α-helix | 34-37 | 4 | |
| α-helix | 41-72 | 32 | |
| α-helix | 73-75 | 3 | |
| β-strand | 77-79 | 3 | 2 |
| α-helix | 81-95 | 15 | |
| α-helix | 97-105 | 9 | |
| α-helix | 114-147 | 34 | |
| α-helix | 149-151 | 3 | |
| α-helix | 154-182 | 29 | |
| β-strand | 183-187 | 5 | 3 |
| β-strand | 194-198 | 5 | 3 |
| α-helix | 205-217 | 13 | |
| α-helix | 218-222 | 5 | |
| α-helix | 223-241 | 19 | |
| α-helix | 243-248 | 6 | |
| α-helix | 251-279 | 29 | |
| α-helix | 284-285 | 2 | |
| α-helix | 287-310 | 24 | |
| α-helix | 312-315 | 4 | |
| α-helix | 320-328 | 9 | |
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 | 4 |
| β-strand | 28-31 | 4 | 1 |
| β-strand | 35-36 | 2 | 1 |
| β-strand | 39-41 | 3 | 4 |
| β-strand | 48-50 | 3 | 4 |
| α-helix | 56-67 | 12 | |
Chain C: 0 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-8 | 4 | 5 |
| β-strand | 11-13 | 3 | 6 |
| β-strand | 19-26 | 8 | 5 |
| β-strand | 34-39 | 6 | 6 |
| β-strand | 46-50 | 5 | 6 |
| β-strand | 54-55 | 2 | 6 |
| β-strand | 64-66 | 3 | 5 |
| β-strand | 72-77 | 6 | 5 |
| β-strand | 86-91 | 6 | 6 |
| β-strand | 98-99 | 2 | 6 |
| β-strand | 103-106 | 4 | 6 |
Chain D: 1 helix, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-10 | 5 | 7 |
| β-strand | 20-28 | 9 | 7 |
| β-strand | 36-42 | 7 | 8 |
| β-strand | 48-55 | 8 | 8 |
| β-strand | 61-63 | 3 | 8 |
| α-helix | 65-67 | 3 | |
| β-strand | 72-76 | 5 | 7 |
| β-strand | 81-87 | 7 | 7 |
| β-strand | 95-102 | 8 | 8 |
| β-strand | 106 | 1 | 9 |
| β-strand | 111 | 1 | 9 |
| β-strand | 117-118 | 2 | 8 |
| β-strand | 122-124 | 3 | 8 |
Chain E: 2 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-8 | 4 | 10 |
| β-strand | 11-12 | 2 | 11 |
| α-helix | 14-15 | 2 | |
| β-strand | 20-26 | 7 | 10 |
| β-strand | 34-39 | 6 | 11 |
| β-strand | 46-49 | 4 | 11 |
| β-strand | 57 | 1 | 12 |
| β-strand | 59 | 1 | 12 |
| β-strand | 63-66 | 4 | 10 |
| β-strand | 71-76 | 6 | 10 |
| β-strand | 86-91 | 6 | 11 |
| α-helix | 97 | 1 | |
| β-strand | 98-99 | 2 | 11 |
| β-strand | 103-105 | 3 | 11 |
Chain F: 2 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-10 | 5 | 13 |
| β-strand | 15 | 1 | 14 |
| β-strand | 20-28 | 9 | 13 |
| α-helix | 32-34 | 3 | |
| β-strand | 35-42 | 8 | 15 |
| β-strand | 48-54 | 7 | 15 |
| β-strand | 61-63 | 3 | 15 |
| α-helix | 65-67 | 3 | |
| β-strand | 72-76 | 5 | 13 |
| β-strand | 81-87 | 7 | 13 |
| β-strand | 95-103 | 9 | 15 |
| β-strand | 111-113 | 3 | 2 |
| β-strand | 117 | 1 | 15 |
| β-strand | 124-126 | 3 | 15 |
| β-strand | 128 | 1 | 14 |
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 | |
| CID24 Fab light chain | E | protein | 215 | Homo sapiens | |
| CID24 Fab heavy chain | F | protein | 238 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>7SK3_1 Atypical chemokine receptor 3 (chains A)
GAPDLHLFDYSEPGNFSDISWPCNSSDCIVVDTVMCPNMPNKSVLLYTLSFIYIFIFVIG
MIANSVVVWVNIQAKTTGYDTHCYILNLAIADLWVVLTIPVWVVSLVQHNQWPMGELTCK
VTHLIFSINLFGSIFFLTCMSVDRYLSITYFTNTPSSRKKMVRRVVCILVWLLAFCVSLP
DTYYLKTVTSASNNETYCRSFYPEHSIKEWLIGMELVSVVLGFAVPFSIIAVFYFLLARA
ISASSDQEKHSSRKIIFSYVVVFLVCWLPYHVAVLLDIFSILHYIPFTCRLEHALFTALH
VTQCLSLVHCCVNPVLYSFINRNYRYELMKAFIFKYSAKTGLTKLIDASRVSETEYSALE
QSTKGRPLEVLFQGPHHHHHHHHHHDYKDDDDK
Sequence of entity 2 (B), FASTA
>7SK3_2 Stromal cell-derived factor 1 (chains B)
KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQE
YLEKALNK
Sequence of entity 3 (C), FASTA
>7SK3_3 CID25 Fab light chain (chains C)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQYYYPLFTFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Sequence of entity 4 (D), FASTA
>7SK3_4 CID25 Fab heavy chain (chains D)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNFSYSSIHWVRQAPGKGLEWVAYIYSSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARVYPWWYYKYYHGALDYWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
Sequence of entity 5 (E), FASTA
>7SK3_5 CID24 Fab light chain (chains E)
SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVP
SRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYYYPITFGQGTKVEIKRTVAAPSVFIFP
PSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Sequence of entity 6 (F), FASTA
>7SK3_6 CID24 Fab heavy chain (chains F)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNISSSSIHWVRQAPGKGLEWVASISPSYGY
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARVSYWDWTWGWSKYEGMDYW
GQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CLR | Cholesterol | C27 H46 O | 8 |
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…
- 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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