4XT1: Nanobody-bound viral GPCR

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.

Method: X-ray diffraction
Resolution: 2.89 Å
Organisms: Cytomegalovirus, Homo sapiens, Vicugna pacos
Chains: 3
Atoms: 3,978
Mol. weight: 69.67 kDa
Ligands: SIN, OLC, CLR
Released: 4 Mar 2015

Explore 4XT1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

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.

Chain A: 14 helices, 3 β-strands

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

Chain B: 3 helices, 4 β-strands

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

Chain C: 1 helix, 13 β-strands

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

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>4XT1_1 G-protein coupled receptor homolog US28 (chains A)
DYKDDDDAMTPTTTTAELTTEFDYDEDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNF
LVIFTITWRRRIQCSGDVYFINLAAADLLFVCTLPLWMQYLLDHNSLASVPCTLLTACFY
VAMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQ
CMTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIA
VVLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYV
FVGTKFRQELHCLLAEFRQRLFSRDVSWYHSMSFSRRSSPSRRETSSDTLSDEVCRVSQI
IP

Sequence of entity 2 (B), FASTA

>4XT1_2 Fractalkine (chains B)
QHHGVTKCAITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKD
AMQHLDRQAAALTRNGGSGSGSAAALEVLFQ

Sequence of entity 3 (C), FASTA

>4XT1_3 nanobody 7 (chains C)
GPGSQVQLVESGGGLVRPGGSLRLSCAASGSIFTIYAMGWYRQAPGKQRELVARITFGGD
TNYADSVKGRFTISRDNAKNAVYLQMNSLKPEDTAVYYCNAEETIVEEADYWGQGTQVTV
SSRAAAHHHHHHHH

Ligands and cofactors

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.

Primary citation

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:

9XIX 2.58 Å, Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the C-state
9XH2 2.6 Å, Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the E-state
9XJP 2.74 Å, Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the E-state, chemokine domain fully…
9XJ5 2.81 Å, Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the C-state, full chemokine domain…
9XIY 2.86 Å, Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the T2C-state
9XJ7 2.89 Å, Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the C'-state with AHD visible
7RKM 3.5 Å, Structure of CX3CL1-US28-Gi-scFv16 in C-state
7RKN 3.6 Å, Structure of CX3CL1-US28-Gi-scFv16 in OC-state
4XT3 3.8 Å, Structure of a viral GPCR bound to human chemokine CX3CL1
7RKF 4.0 Å, Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state

Browse structure collections

About this viewer

MolViewer shows 4XT1 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.