8U4O: CXCL12-bound CXCR4/Gi complex
Structure of CXCL12-bound CXCR4/Gi complex. Determined by electron microscopy at 3.29 Å resolution. Released 13 Mar 2024.
- Method
- Electron microscopy
- Resolution
- 3.29 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 7,401
- Mol. weight
- 167.42 kDa
- Ligands
- CLR
- Released
- 13 Mar 2024
Explore 8U4O in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8U4O contains 32 α-helices and 46 β-strands across 5 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: 8 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-30 | 24 | |
| β-strand | 34-40 | 7 | 2 |
| α-helix | 47-52 | 6 | |
| β-strand | 185-190 | 6 | 2 |
| β-strand | 195-200 | 6 | 2 |
| α-helix | 208-210 | 3 | |
| α-helix | 212-215 | 4 | |
| β-strand | 220-226 | 7 | 2 |
| β-strand | 233 | 1 | 3 |
| β-strand | 241 | 1 | 3 |
| α-helix | 242-254 | 13 | |
| β-strand | 263-269 | 7 | 2 |
| α-helix | 271-280 | 10 | |
| α-helix | 296-308 | 13 | |
| β-strand | 319-323 | 5 | 2 |
| α-helix | 331-350 | 20 | |
Chain B: 4 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-25 | 19 | |
| α-helix | 30-33 | 4 | |
| α-helix | 38-43 | 6 | |
| β-strand | 47-51 | 5 | 4 |
| β-strand | 58-63 | 6 | 5 |
| β-strand | 70-74 | 5 | 5 |
| β-strand | 78-82 | 5 | 5 |
| β-strand | 89-94 | 6 | 5 |
| β-strand | 100-105 | 6 | 6 |
| β-strand | 111-116 | 6 | 6 |
| β-strand | 121-125 | 5 | 6 |
| β-strand | 134-139 | 6 | 6 |
| β-strand | 146-151 | 6 | 7 |
| β-strand | 157-161 | 5 | 7 |
| β-strand | 165-168 | 4 | 7 |
| β-strand | 178-181 | 4 | 7 |
| β-strand | 187-192 | 6 | 8 |
| β-strand | 199-203 | 5 | 8 |
| β-strand | 207-210 | 4 | 8 |
| β-strand | 220-223 | 4 | 8 |
| β-strand | 229-234 | 6 | 9 |
| β-strand | 240-245 | 6 | 9 |
| β-strand | 250-254 | 5 | 9 |
| β-strand | 262-264 | 3 | 9 |
| α-helix | 272 | 1 | |
| β-strand | 273-277 | 5 | 10 |
| β-strand | 284-289 | 6 | 10 |
| β-strand | 294-298 | 5 | 10 |
| β-strand | 307 | 1 | 10 |
| β-strand | 315-320 | 6 | 4 |
| β-strand | 327-331 | 5 | 4 |
| β-strand | 336-339 | 4 | 4 |
Chain C: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-23 | 11 | |
| α-helix | 30-43 | 14 | |
| α-helix | 53-55 | 3 | |
Chain J: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 15 | 1 | 11 |
| α-helix | 20-22 | 3 | |
| β-strand | 23 | 1 | 12 |
| β-strand | 28-29 | 2 | 13 |
| β-strand | 37-38 | 2 | 13 |
| β-strand | 40-41 | 2 | 14 |
| β-strand | 42 | 1 | 12 |
| β-strand | 48-49 | 2 | 14 |
| β-strand | 51 | 1 | 11 |
| α-helix | 56-63 | 8 | |
Chain R: 15 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-64 | 34 | |
| α-helix | 69-70 | 2 | |
| α-helix | 72-88 | 17 | |
| α-helix | 91-99 | 9 | |
| α-helix | 105-138 | 34 | |
| α-helix | 147-153 | 7 | |
| α-helix | 157-161 | 5 | |
| α-helix | 162-167 | 6 | |
| α-helix | 169-173 | 5 | |
| β-strand | 176-180 | 5 | 1 |
| β-strand | 183-187 | 5 | 1 |
| α-helix | 195-208 | 14 | |
| α-helix | 210-225 | 16 | |
| α-helix | 232-266 | 35 | |
| α-helix | 274-291 | 18 | |
| α-helix | 294-302 | 9 | |
| α-helix | 307-317 | 11 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| C-X-C chemokine receptor type 4 | R | protein | 632 | Homo sapiens | P42212 (AlphaFold model), P61073 (AlphaFold model) |
| Guanine nucleotide-binding protein G(i) subunit alpha-1 | A | protein | 365 | Homo sapiens | P63096 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | B | protein | 350 | Homo sapiens | P62873 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | C | protein | 71 | Homo sapiens | P59768 |
| Stromal cell-derived factor 1 | J | protein | 68 | Homo sapiens | P48061 |
Sequence of entity 1 (R), FASTA
>8U4O_1 C-X-C chemokine receptor type 4 (chains R)
MKTIIALSYIFCLVFAGAPEGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLP
TIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANW
YFGNFLCKAVHVIYTVSLYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWI
PALLLTIPDFIFANVSEADDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCII
ISKLSHSKGHQKRKALKTTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHK
WISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVST
ESESSSFHSSGRPLEVLFQGPGGGGSVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGE
GDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQ
ERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMA
DKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEK
RDHMVLLEFVTAAGITLGMDELYKDYKDDDDK
Sequence of entity 2 (A), FASTA
>8U4O_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MHHHHHHGGGGSGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKCTI
VKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFV
LAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIP
TQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVTAQRSERKKWIHCFEGVTAIIFCVALSD
YDLVLAEDEEMNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPE
YAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLK
DCGLF
Sequence of entity 3 (B), FASTA
>8U4O_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN
Sequence of entity 4 (C), FASTA
>8U4O_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 5 (J), FASTA
>8U4O_5 Stromal cell-derived factor 1 (chains J)
KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQE
YLEKALNK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CLR | Cholesterol | C27 H46 O | 1 |
Primary citation
Structural insights into CXCR4 modulation and oligomerization. Saotome, K., McGoldrick, L.L., Ho, J.H. et al. Nat Struct Mol Biol (2025) 32:315-325. DOI 10.1038/s41594-024-01397-1 · PubMed
Other PDB entries of the same protein (UniProt P42212 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6L27 0.77 Å, X-ray crystal structure of the mutant green fluorescent protein
- 6JGJ 0.78 Å, Crystal structure of the F99S/M153T/V163A/E222Q variant of GFP at 0.78 A
- 6KL0 0.8 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of perdeuterated GFP at pD 7.0
- 6JGI 0.85 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of GFP at 0.85 A
- 6KL1 0.85 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of non-deuterated GFP at pD 8.5
- 2WUR 0.9 Å, Atomic resolution structure of GFP measured on a rotating anode
- 6KKZ 0.9 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of perdeuterated GFP at pD 8.5
- 6JGH 0.94 Å, Crystal structure of the F99S/M153T/V163A/T203I variant of GFP at 0.94 A
- 4AS8 1.02 Å, X-ray structure of the cyan fluorescent protein Cerulean cryoprotected with ethylene…
- 5OXC 1.02 Å, Structure of Cerulean Fluorescent Protein at 1.02 Angstrom resolution
- 7PCA 1.05 Å, Functional and structural characterization of redox sensitive superfolder green…
- 4GF6 1.1 Å, crystal structure of GFP with cuprum bound at the Incorporated metal Chelating Amino…
Browse structure collections
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