7XBX: Human chemokine receptor CX3CR1

Cryo-EM structure of the human chemokine receptor CX3CR1 in complex with CX3CL1 and Gi1. Determined by electron microscopy at 3.4 Å resolution. Released 13 Jul 2022.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,616
Mol. weight: 138.89 kDa
Ligands: CLR
Released: 13 Jul 2022

Explore 7XBX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XBX contains 27 α-helices and 41 β-strands across 4 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 C: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	36-40	5	1
α-helix	46-50	5
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-212	5
α-helix	213-215	3
β-strand	220-226	7	1
α-helix	227-229	3
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-278	8
α-helix	296-310	15
β-strand	320-323	4	1
α-helix	328-347	20

Chain D: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
α-helix	38-39	2
β-strand	47-51	5	2
β-strand	61-63	3	3
β-strand	69-73	5	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	103-105	3	4
β-strand	111-114	4	4
β-strand	116	1	5
β-strand	120-125	6	4
β-strand	135-140	6	4
α-helix	145	1
β-strand	146-150	5	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	176-180	5	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	218-223	6	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	262-265	4	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	315	1	9
β-strand	319-320	2	2
β-strand	327-330	4	2
β-strand	331	1	9
β-strand	336-339	4	2

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	30-43	14

Chain R: 14 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	10
α-helix	30-33	4
β-strand	42	1	10
α-helix	56-65	10
α-helix	128-159	32
α-helix	167-195	29
α-helix	203-234	32
α-helix	236-242	7
α-helix	245-268	24
β-strand	271-272	2	11
β-strand	277-278	2	11
α-helix	283-285	3
α-helix	288-298	11
α-helix	299-303	5
α-helix	304-323	20
α-helix	330-359	30
α-helix	367-398	32
α-helix	401-409	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	C	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D	protein	346	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E	protein	71	Homo sapiens	P59768 (AlphaFold model)
Processed fractalkine,CX3C chemokine receptor 1	R	protein	463	Homo sapiens	P49238 (AlphaFold model), P78423

Sequence of entity 1 (C), FASTA

>7XBX_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKCTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVTAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (D), FASTA

>7XBX_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains D)
HHHHHHMSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGH
LAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVAC
GGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETG
QQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICF
FPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNC
NVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (E), FASTA

>7XBX_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains E)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>7XBX_4 Processed fractalkine,CX3C chemokine receptor 1 (chains R)
QHHGVTKCNITCSKMTSKIPVALLIHYQQNQASCCKRAIILETRQHRLFCADPKEQWVKD
AMQHLDRQAAALTRNGSGSGSGSGSGSGSGSGSGSGSGSGSGSDQFPESVTENFEYDDLA
EACYIGDIVVFGTVFLSIFYSVIFAIGLVGNLLVVFALTNSKKPKSVTDIYLLNLALSDL
LFVATLPFWTHYLINEKGLHNAMCKFTTAFFFIGFFGSIFFLTVISIDRYLAIVLAANSM
NNRTVQHGVTISLGVWAAAILVAAPQFMFTKQKENECCGDYPEVLQEIWPVLRNVETNFL
GFLLPLLIMSYCYFRIIQTLFSSKNHKKAKAIKLILLVVIVFFLFWTPYNVVIFLETLKL
YDFFPSCDMRKDLRLALSVTETVAFSHCCLNPLIYAFAGEKFRRYLYHLYGKCLAVLEFL
EVLFQGPWSHPQFEKGGGSGGGSGGSAWSHPQFEKDYKDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2

Primary citation

Activation of the human chemokine receptor CX3CR1 regulated by cholesterol. Lu, M., Zhao, W., Han, S. et al. Sci Adv (2022) 8:eabn8048-eabn8048. DOI 10.1126/sciadv.abn8048 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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