9ME1: HCXCR4-CXCL12 complex with 1:1 stoichiometry
hCXCR4-CXCL12 complex with 1:1 stoichiometry. Determined by electron microscopy at 3.37 Å resolution. Released 10 Sept 2025.
- Method
- Electron microscopy
- Resolution
- 3.37 Å
- Organism
- Homo sapiens
- Chains
- 16
- Atoms
- 21,155
- Mol. weight
- 403.46 kDa
- Released
- 10 Sept 2025
Explore 9ME1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9ME1 contains 145 α-helices and 47 β-strands across 16 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: 18 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-59 | 23 | |
| α-helix | 60-65 | 6 | |
| α-helix | 73-99 | 27 | |
| α-helix | 106-138 | 33 | |
| 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 | 169-174 | 6 | |
| β-strand | 175-179 | 5 | 2 |
| β-strand | 184-188 | 5 | 2 |
| α-helix | 193-204 | 12 | |
| α-helix | 205-209 | 5 | |
| α-helix | 210-226 | 17 | |
| α-helix | 227-229 | 3 | |
| α-helix | 238-266 | 29 | |
| α-helix | 273-290 | 18 | |
| α-helix | 291-294 | 4 | |
| α-helix | 298-304 | 7 | |
Chain B: 17 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-60 | 26 | |
| α-helix | 61-65 | 5 | |
| α-helix | 73-99 | 27 | |
| α-helix | 105-139 | 35 | |
| 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 | 1 |
| β-strand | 186-188 | 3 | 1 |
| α-helix | 193-204 | 12 | |
| α-helix | 205-209 | 5 | |
| α-helix | 210-226 | 17 | |
| α-helix | 233-235 | 3 | |
| α-helix | 238-265 | 28 | |
| α-helix | 275-290 | 16 | |
| α-helix | 291-294 | 4 | |
| α-helix | 297-303 | 7 | |
Chain C: 17 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-59 | 23 | |
| α-helix | 60-65 | 6 | |
| α-helix | 74-99 | 26 | |
| α-helix | 105-138 | 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 | 5 |
| β-strand | 186-188 | 3 | 5 |
| α-helix | 193-204 | 12 | |
| α-helix | 205-209 | 5 | |
| α-helix | 210-225 | 16 | |
| α-helix | 233-235 | 3 | |
| α-helix | 238-265 | 28 | |
| α-helix | 275-290 | 16 | |
| α-helix | 291-294 | 4 | |
| α-helix | 297-303 | 7 | |
Chain D: 18 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-59 | 25 | |
| α-helix | 60-65 | 6 | |
| α-helix | 73-99 | 27 | |
| α-helix | 105-138 | 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 | 6 |
| β-strand | 186-188 | 3 | 6 |
| α-helix | 193-204 | 12 | |
| α-helix | 205-209 | 5 | |
| α-helix | 210-226 | 17 | |
| α-helix | 233-235 | 3 | |
| α-helix | 238-265 | 28 | |
| α-helix | 266-268 | 3 | |
| α-helix | 275-290 | 16 | |
| α-helix | 291-294 | 4 | |
| α-helix | 297-303 | 7 | |
Chain E: 17 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-59 | 23 | |
| α-helix | 60-65 | 6 | |
| α-helix | 73-88 | 16 | |
| α-helix | 91-99 | 9 | |
| α-helix | 107-138 | 32 | |
| α-helix | 146-153 | 8 | |
| α-helix | 155-166 | 12 | |
| α-helix | 169-173 | 5 | |
| β-strand | 175-177 | 3 | 8 |
| β-strand | 186-188 | 3 | 8 |
| α-helix | 193-204 | 12 | |
| α-helix | 205-209 | 5 | |
| α-helix | 210-225 | 16 | |
| α-helix | 226-228 | 3 | |
| α-helix | 233-235 | 3 | |
| α-helix | 236-265 | 30 | |
| α-helix | 276-289 | 14 | |
| α-helix | 290-294 | 5 | |
| α-helix | 297-303 | 7 | |
Chain F: 1 helix, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-28 | 6 | 4 |
| β-strand | 38-42 | 5 | 4 |
| β-strand | 48-51 | 4 | 4 |
| α-helix | 56-63 | 8 | |
Chain G: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 15 | 1 | 11 |
| β-strand | 23-29 | 7 | 11 |
| β-strand | 37-42 | 6 | 11 |
| β-strand | 48-51 | 4 | 11 |
| α-helix | 56-63 | 8 | |
Chain H: 1 helix, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 15 | 1 | 13 |
| β-strand | 25-28 | 4 | 12 |
| β-strand | 29 | 1 | 14 |
| β-strand | 37 | 1 | 14 |
| β-strand | 40-41 | 2 | 12 |
| β-strand | 48-49 | 2 | 12 |
| β-strand | 51 | 1 | 13 |
| α-helix | 56-62 | 7 | |
6 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| C-X-C chemokine receptor type 4 | A, B, C, D, E, I, K, L | protein | 360 | Homo sapiens | P61073 (AlphaFold model) |
| Stromal cell-derived factor 1 | F, G, H, J, M, N, O, P | protein | 80 | Homo sapiens | P48061 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, I, K, L), FASTA
>9ME1_1 C-X-C chemokine receptor type 4 (chains A, B, C, D, E, I, K, L)
MEGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVI
LVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNL
YSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEA
DDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKT
TVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPI
LYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSSDYKDDDDK
Sequence of entity 2 (F, G, H, J, M, N, O, P), FASTA
>9ME1_2 Stromal cell-derived factor 1 (chains F, G, H, J, M, N, O, P)
KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQE
YLEKALNKRFKMHHHHHHHH
Primary citation
CXCR4 mediated recognition of HIV envelope spike and inhibition by CXCL12. Zhang, Z., Zhang, H., Zheng, L. et al. Nat Commun (2025) 16:8653-8653. DOI 10.1038/s41467-025-63815-2 · 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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