Cryo-EM strucutre of CXCR4 complexed with antagonist HF51116. Determined by electron microscopy at 3.01 Å resolution. Released 26 Feb 2025.
Explore 8ZPL in 3D Show helices and sheets RCSB PDB PDBe
8ZPL contains 20 α-helices and 13 β-strands across 2 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 4-9 | 6 | 1 |
| β-strand | 12-15 | 4 | 2 |
| β-strand | 20-28 | 9 | 1 |
| β-strand | 32-39 | 8 | 3 |
| β-strand | 49-54 | 6 | 3 |
| α-helix | 63-65 | 3 | |
| β-strand | 69-74 | 6 | 1 |
| β-strand | 79-84 | 6 | 1 |
| α-helix | 89-91 | 3 | |
| β-strand | 93-95 | 3 | 2 |
| β-strand | 96-102 | 7 | 3 |
| α-helix | 108-109 | 2 | |
| β-strand | 110-113 | 4 | 3 |
| β-strand | 117-122 | 6 | 2 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 35-60 | 26 | |
| α-helix | 61-65 | 5 | |
| α-helix | 72-88 | 17 | |
| α-helix | 91-99 | 9 | |
| α-helix | 106-139 | 34 | |
| α-helix | 146-153 | 8 | |
| α-helix | 155-156 | 2 | |
| α-helix | 157-161 | 5 | |
| α-helix | 162-166 | 5 | |
| α-helix | 169-173 | 5 | |
| β-strand | 175-177 | 3 | 4 |
| β-strand | 186-188 | 3 | 4 |
| α-helix | 193-204 | 12 | |
| α-helix | 205-209 | 5 | |
| α-helix | 210-226 | 17 | |
| α-helix | 236-274 | 39 | |
| α-helix | 282-299 | 18 | |
| α-helix | 300-304 | 5 | |
| α-helix | 305-313 | 9 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Nb6 nanobody | N | protein | 169 | Lama glama | |
| Soluble cytochrome b562,C-X-C chemokine receptor type 4 | R | protein | 486 | Escherichia coli, Homo sapiens | P61073 (AlphaFold model) |
>8ZPL_1 Nb6 nanobody (chains N) MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAMAQVQLQESGGGLVQAGESLRL SCAASGTIFRLYDMGWYRRVSGNQRELVASITSGGSTKYGDSVKGRFTISRDNAKNTVYL QMSSLKPEDTAVYYCNAEYRTGIWEELLDGWGQGTQVTVSSHHHHHHHH
>8ZPL_2 Soluble cytochrome b562,C-X-C chemokine receptor type 4 (chains R) MKTIIALSYIFCLVFADYKDDDDKGSADLEDNWETLNDNLKVIEKADNAAQVKDALTKMR AAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQL KTTRNAYIQKYLLVPRGSMEGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLP TIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANW YFGNFLCKAVHVIYTVNLYSSVWILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWI PALLLTIPDFIFANVSEADDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCII ISRLKSVRLLSGSREKDRNLRRITRPTVILILAFFACWLPYYIGISIDSFILLEIIKQGC EFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSGRPLEVLFQGPHHHH HHHHHH
| ID | Name | Formula | Copies |
|---|---|---|---|
| CLR | Cholesterol | C27 H46 O | 2 |
| A1D8K | (2S)-N-[[4-[[3-(cyclohexylamino)propylamino]methyl]phenyl]methyl]-5-(diaminomet… | C29 H46 N8 O | 1 |
Structural mechanisms underlying the modulation of CXCR4 by diverse small-molecule antagonists. Sang, X., Jiao, H., Meng, Q. et al. Proc Natl Acad Sci U S A (2025) 122:e2425795122-e2425795122. DOI 10.1073/pnas.2425795122 · PubMed
Other PDB entries of the same protein (UniProt P61073 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 8ZPL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.