5WB2: US28

US28 bound to engineered chemokine CX3CL1.35 and nanobodies. Determined by X-ray diffraction at 3.5 Å resolution. Released 13 Jun 2018.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Human cytomegalovirus, Lama glama, Homo sapiens
Chains: 3
Atoms: 4,907
Mol. weight: 77.4 kDa
Ligands: CLR, OLC, ZN
Released: 13 Jun 2018

Explore 5WB2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WB2 contains 19 α-helices and 35 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: 16 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	23-24	2	1
α-helix	26-59	34
α-helix	67-83	17
α-helix	86-94	9
α-helix	96-98	3
α-helix	101-133	33
α-helix	141-163	23
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	296-306	11
β-strand	1004-1007	4	3
β-strand	1010-1012	3	4
β-strand	1017-1024	8	3
β-strand	1031-1039	9	4
β-strand	1045-1052	8	4
β-strand	1057-1059	3	4
β-strand	1064	1	3
β-strand	1067-1072	6	3
β-strand	1077-1083	7	3
α-helix	1087-1089	3
β-strand	1091-1099	9	4
β-strand	1107-1108	2	4
β-strand	1109	1	3
β-strand	1112-1116	5	4
β-strand	1120-1122	3	5

Chain B: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	1
β-strand	24-29	6	6
β-strand	39-43	5	6
β-strand	48-51	4	6
α-helix	56-69	14

Chain D: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-11	2	8
β-strand	17-25	9	7
β-strand	33-38	6	5
β-strand	46-51	6	5
β-strand	58-60	3	5
β-strand	68-71	4	7
α-helix	75-77	3
β-strand	78-84	7	7
α-helix	88-90	3
β-strand	92-94	3	8
β-strand	95-99	5	5
β-strand	103-105	3	9
β-strand	107-108	2	9
β-strand	114-116	3	5
β-strand	123-126	4	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope protein US28, nanobody 7 fusion protein	A	protein	460	Human cytomegalovirus, Lama glama	P69333
CX3CL1 protein	B	protein	76	Homo sapiens	P78423 (AlphaFold model)
nanobody B1	D	protein	131	synthetic construct

Sequence of entity 1 (A), FASTA

>5WB2_1 Envelope protein US28, nanobody 7 fusion protein (chains A)
YKDDDDAMTPTTTTAELTTEFDYDEDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNFL
VIFTITWRRRIQCSGDVYFINLAAADLLFVCTLPLWMQYLLDHNSLASVPCTLLTACFYV
AMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQC
MTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIAV
VLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYVF
VGTKFRQELHCLLAEFRLVPRGSGGSGGSLVPRGSQVQLVESGGGLVRPGGSLRLSCAAS
GSIFTIYAMGWYRQAPGKQRELVARITFGGDTNYADSVKGRFTISRDNAKNAVYLQMNSL
KPEDTAVYYCNAEETIVEEADYWGQGTQVTVSSRALEVLF

Sequence of entity 2 (B), FASTA

>5WB2_2 CX3CL1 protein (chains B)
LLPHANYCAITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKD
AMQHLDRQAAALTRNG

Sequence of entity 3 (D), FASTA

>5WB2_3 nanobody B1 (chains D)
QLQLVESGGGLVQPGGSLRLSCAASGYSLEYYAIGWFRQAPGKEREGVSCISTSVGSTKY
ADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCGADLSTFYGGNYYCGDRGIYDYYG
QGTQVTVSSRG

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	4
ZN	Zinc ion	Zn	1

Water and common crystallization additives (MES) are not listed.

Primary citation

Viral GPCR US28 can signal in response to chemokine agonists of nearly unlimited structural degeneracy. Miles, T.F., Spiess, K., Jude, K.M. et al. Elife (2018) 7. DOI 10.7554/eLife.35850 · PubMed

Other PDB entries of the same protein (UniProt P69333), best resolution first:

5WB1 3.51 Å, Ligand-free US28 with stabilizing intracellular nanobody

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