22XC: CXCR4
Structure of CXCR4 in complex with a de-novo designed mini-protein antagonist. Determined by electron microscopy at 3.28 Å resolution. Released 22 Apr 2026.
- Method
- Electron microscopy
- Resolution
- 3.28 Å
- Organisms
- synthetic construct, Homo sapiens
- Chains
- 6
- Atoms
- 8,623
- Mol. weight
- 170.24 kDa
- Ligands
- CLR, D21
- Released
- 22 Apr 2026
Explore 22XC in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
22XC contains 60 α-helices and 19 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: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-8 | 7 | 1 |
| α-helix | 10-31 | 22 | |
| β-strand | 34-39 | 6 | 1 |
| β-strand | 44-50 | 7 | 1 |
| α-helix | 52-72 | 21 | |
Chain B: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 2 |
| β-strand | 7-8 | 2 | 2 |
| α-helix | 10-31 | 22 | |
| β-strand | 34-40 | 7 | 2 |
| β-strand | 43-50 | 8 | 2 |
| α-helix | 52-72 | 21 | |
Chain C: 18 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-60 | 27 | |
| α-helix | 61-65 | 5 | |
| α-helix | 73-89 | 17 | |
| α-helix | 91-99 | 9 | |
| α-helix | 107-138 | 32 | |
| α-helix | 146-150 | 5 | |
| α-helix | 151-155 | 5 | |
| α-helix | 156 | 1 | |
| α-helix | 157-161 | 5 | |
| α-helix | 162-166 | 5 | |
| α-helix | 169-173 | 5 | |
| β-strand | 175-180 | 6 | 3 |
| β-strand | 183-188 | 6 | 3 |
| β-strand | 190 | 1 | 2 |
| α-helix | 193-204 | 12 | |
| α-helix | 205-209 | 5 | |
| α-helix | 210-226 | 17 | |
| α-helix | 239-266 | 28 | |
| α-helix | 275-290 | 16 | |
| α-helix | 291-293 | 3 | |
| α-helix | 294-304 | 11 | |
Chain D: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-8 | 7 | 4 |
| α-helix | 10-31 | 22 | |
| β-strand | 34-40 | 7 | 4 |
| β-strand | 43-50 | 8 | 4 |
| α-helix | 52-72 | 21 | |
Chain G: 18 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-60 | 27 | |
| α-helix | 61-65 | 5 | |
| α-helix | 73-88 | 16 | |
| α-helix | 91-99 | 9 | |
| α-helix | 107-138 | 32 | |
| α-helix | 146-150 | 5 | |
| α-helix | 151-155 | 5 | |
| α-helix | 156 | 1 | |
| α-helix | 157-161 | 5 | |
| α-helix | 162-166 | 5 | |
| α-helix | 169-173 | 5 | |
| β-strand | 175-180 | 6 | 5 |
| β-strand | 183-188 | 6 | 5 |
| β-strand | 190 | 1 | 4 |
| α-helix | 193-204 | 12 | |
| α-helix | 205-209 | 5 | |
| α-helix | 210-226 | 17 | |
| α-helix | 239-266 | 28 | |
| α-helix | 275-290 | 16 | |
| α-helix | 291-293 | 3 | |
| α-helix | 294-304 | 11 | |
Chain R: 18 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-60 | 27 | |
| α-helix | 61-65 | 5 | |
| α-helix | 73-89 | 17 | |
| α-helix | 91-99 | 9 | |
| α-helix | 107-138 | 32 | |
| α-helix | 146-150 | 5 | |
| α-helix | 151-155 | 5 | |
| α-helix | 156 | 1 | |
| α-helix | 157-161 | 5 | |
| α-helix | 162-166 | 5 | |
| α-helix | 169-173 | 5 | |
| β-strand | 175-180 | 6 | 6 |
| β-strand | 183-188 | 6 | 6 |
| β-strand | 190 | 1 | 1 |
| α-helix | 193-204 | 12 | |
| α-helix | 205-209 | 5 | |
| α-helix | 210-226 | 17 | |
| α-helix | 238-266 | 29 | |
| α-helix | 275-290 | 16 | |
| α-helix | 291-293 | 3 | |
| α-helix | 294-304 | 11 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| dCX001 binder antagonist | A, B, D | protein | 87 | synthetic construct | |
| C-X-C chemokine receptor type 4 | C, G, R | protein | 408 | Homo sapiens | P61073 (AlphaFold model) |
Sequence of entity 1 (A, B, D), FASTA
>22XC_1 dCX001 binder antagonist (chains A, B, D)
MSGMVLKAVSMPTGIYSKLKKEYGEEIEKKAKELGVKISYGYRNGEMLIGFSGKKEEVDK
LVKYVKKIVTEISRKRNGSLEHHHHHH
Sequence of entity 2 (C, G, R), FASTA
>22XC_2 C-X-C chemokine receptor type 4 (chains C, G, R)
MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSEGI
SIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMG
YQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNLYSSV
LILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADDRY
ICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVIL
ILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAF
LGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CLR | Cholesterol | C27 H46 O | 3 |
| D21 | (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate | C37 H71 O8 P | 3 |
Primary citation
De novo design of miniproteins targeting GPCRs. Muratspahic, E., Feldman, D., Kim, D.E. et al. Nature (2026) 656:1044-1053. DOI 10.1038/s41586-026-10656-8 · PubMed
Other PDB entries of the same protein (UniProt P61073 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3ODU 2.5 Å, The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule…
- 9UPV 2.7 Å, Cryo-EM structure of CXCR4 complexed with agonist SDVX1
- 8U4N 2.72 Å, Structure of Apo CXCR4/Gi complex
- 9UPU 2.8 Å, Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a
- 8K3Z 2.81 Å, Cryo-EM structure of CXCR4 in complex with CXCL12
- 3OE0 2.9 Å, Crystal structure of the CXCR4 chemokine receptor in complex with a cyclic peptide…
- 9MDU 2.9 Å, Human CXCR4 tetramer
- 8YU7 3.01 Å, Cryo-EM structure of CXCR4 tetramer
- 8ZPL 3.01 Å, Cryo-EM strucutre of CXCR4 complexed with antagonist HF51116
- 3OE8 3.1 Å, Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule…
- 3OE9 3.1 Å, Crystal structure of the chemokine CXCR4 receptor in complex with a small molecule…
- 4RWS 3.1 Å, Crystal structure of CXCR4 and viral chemokine antagonist vMIP-II complex (PSI Community…
Browse structure collections
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