Structure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1. Determined by X-ray diffraction at 2.89 Å resolution. Released 4 Mar 2015.
Explore 4XT1 in 3D Show helices and sheets RCSB PDB PDBe
4XT1 contains 18 α-helices and 20 β-strands across 3 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 | 23-24 | 2 | 1 |
| α-helix | 26-59 | 34 | |
| α-helix | 67-83 | 17 | |
| α-helix | 86-94 | 9 | |
| α-helix | 104-133 | 30 | |
| α-helix | 141-157 | 17 | |
| α-helix | 160-163 | 4 | |
| β-strand | 166-169 | 4 | 2 |
| β-strand | 172-175 | 4 | 2 |
| α-helix | 184-193 | 10 | |
| α-helix | 194-198 | 5 | |
| α-helix | 199-215 | 17 | |
| α-helix | 223-255 | 33 | |
| α-helix | 263-280 | 18 | |
| α-helix | 283-287 | 5 | |
| α-helix | 288-292 | 5 | |
| α-helix | 296-308 | 13 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 10-11 | 2 | 1 |
| β-strand | 24-29 | 6 | 3 |
| α-helix | 30-31 | 2 | |
| α-helix | 32-34 | 3 | |
| β-strand | 39-43 | 5 | 3 |
| β-strand | 48-51 | 4 | 3 |
| α-helix | 56-67 | 12 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 4-7 | 4 | 4 |
| β-strand | 10-11 | 2 | 5 |
| β-strand | 17-24 | 8 | 4 |
| β-strand | 31-39 | 9 | 5 |
| β-strand | 45-52 | 8 | 5 |
| β-strand | 57-59 | 3 | 5 |
| β-strand | 64 | 1 | 4 |
| β-strand | 67-72 | 6 | 4 |
| β-strand | 77-83 | 7 | 4 |
| α-helix | 87-89 | 3 | |
| β-strand | 91-99 | 9 | 5 |
| β-strand | 107-108 | 2 | 5 |
| β-strand | 109 | 1 | 4 |
| β-strand | 112-115 | 4 | 5 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| G-protein coupled receptor homolog US28 | A | protein | 362 | Cytomegalovirus | P69332 |
| Fractalkine | B | protein | 91 | Homo sapiens | P78423 (AlphaFold model) |
| nanobody 7 | C | protein | 134 | Vicugna pacos |
>4XT1_1 G-protein coupled receptor homolog US28 (chains A) DYKDDDDAMTPTTTTAELTTEFDYDEDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNF LVIFTITWRRRIQCSGDVYFINLAAADLLFVCTLPLWMQYLLDHNSLASVPCTLLTACFY VAMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQ CMTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIA VVLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYV FVGTKFRQELHCLLAEFRQRLFSRDVSWYHSMSFSRRSSPSRRETSSDTLSDEVCRVSQI IP
>4XT1_2 Fractalkine (chains B) QHHGVTKCAITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKD AMQHLDRQAAALTRNGGSGSGSAAALEVLFQ
>4XT1_3 nanobody 7 (chains C) GPGSQVQLVESGGGLVRPGGSLRLSCAASGSIFTIYAMGWYRQAPGKQRELVARITFGGD TNYADSVKGRFTISRDNAKNAVYLQMNSLKPEDTAVYYCNAEETIVEEADYWGQGTQVTV SSRAAAHHHHHHHH
| ID | Name | Formula | Copies |
|---|---|---|---|
| SIN | Succinic acid | C4 H6 O4 | 1 |
| OLC | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate | C21 H40 O4 | 6 |
| CLR | Cholesterol | C27 H46 O | 2 |
Water and common crystallization additives (UNL) are not listed.
Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor. Burg, J.S., Ingram, J.R., Venkatakrishnan, A.J. et al. Science (2015) 347:1113-1117. DOI 10.1126/science.aaa5026 · PubMed
Other PDB entries of the same protein (UniProt P69332), best resolution first:
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