9MEU: CXCR4 tetramer
CXCR4 tetramer bound to 4 CXCL12 dimers. Determined by electron microscopy at 3.46 Å resolution. Released 10 Sept 2025.
- Method
- Electron microscopy
- Resolution
- 3.46 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 12,027
- Mol. weight
- 240.32 kDa
- Released
- 10 Sept 2025
Explore 9MEU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9MEU contains 80 α-helices and 41 β-strands across 12 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 | 275-290 | 16 | |
| α-helix | 291-294 | 4 | |
| α-helix | 298-304 | 7 | |
Chain B: 18 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-60 | 24 | |
| α-helix | 61-65 | 5 | |
| α-helix | 73-99 | 27 | |
| α-helix | 107-138 | 32 | |
| α-helix | 146-149 | 4 | |
| α-helix | 150-154 | 5 | |
| α-helix | 155-156 | 2 | |
| α-helix | 157-161 | 5 | |
| α-helix | 162-166 | 5 | |
| α-helix | 169-174 | 6 | |
| 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 | 37-60 | 24 | |
| 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 | 169-174 | 6 | |
| β-strand | 175-177 | 3 | 5 |
| β-strand | 186-188 | 3 | 5 |
| α-helix | 193-204 | 12 | |
| α-helix | 205-209 | 5 | |
| α-helix | 210-226 | 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 D: 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 | 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 | 169-174 | 6 | |
| 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 | 291-293 | 3 | |
| α-helix | 294-303 | 10 | |
Chain F: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-28 | 6 | 4 |
| α-helix | 29 | 1 | |
| β-strand | 38-42 | 5 | 4 |
| β-strand | 48-51 | 4 | 4 |
| α-helix | 56-62 | 7 | |
Chains G and N: 1 helix, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-29 | 7 | 7 |
| β-strand | 37-42 | 6 | 7 |
| β-strand | 48-51 | 4 | 7 |
| α-helix | 56-62 | 7 | |
Chain H: 1 helix, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 15 | 1 | 9 |
| β-strand | 25-28 | 4 | 8 |
| β-strand | 39-41 | 3 | 8 |
| β-strand | 48-50 | 3 | 8 |
| β-strand | 51 | 1 | 9 |
| α-helix | 56-62 | 7 | |
Chain J: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23 | 1 | 8 |
| β-strand | 26-28 | 3 | 8 |
| β-strand | 38-42 | 5 | 8 |
| β-strand | 47-51 | 5 | 8 |
| α-helix | 56-63 | 8 | |
2 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 | 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), FASTA
>9MEU_1 C-X-C chemokine receptor type 4 (chains A, B, C, D)
MEGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVI
LVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNL
YSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEA
DDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKT
TVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPI
LYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSSDYKDDDDK
Sequence of entity 2 (F, G, H, J, M, N, O, P), FASTA
>9MEU_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…
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