7XBW: Human chemokine receptor CX3CR1

Cryo-EM structure of the human chemokine receptor CX3CR1 in complex with Gi1. Determined by electron microscopy at 2.8 Å resolution. Released 13 Jul 2022.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,663
Mol. weight: 128.79 kDa
Ligands: CLR
Released: 13 Jul 2022

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

Secondary structure: helices and β-sheets

7XBW contains 29 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-39	6	1
β-strand	53	1	1
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-229	3
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	328-348	21

Chain D: 3 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	13-25	13
α-helix	30-33	4
α-helix	38-39	2
β-strand	43	1	2
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78	1	5
β-strand	79-83	5	4
β-strand	88-91	4	4
β-strand	94	1	5
β-strand	103-105	3	6
β-strand	111-114	4	6
β-strand	116	1	7
β-strand	120-125	6	6
β-strand	134-140	7	6
β-strand	146-151	6	7
β-strand	156-161	6	7
β-strand	166-170	5	7
β-strand	176-180	5	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	207-212	6	8
β-strand	218-223	6	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	260-264	5	9
β-strand	273-278	6	2
β-strand	284-289	6	2
β-strand	296-298	3	2
β-strand	304-306	3	2
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain E: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	10-24	15
α-helix	30-43	14
α-helix	45-47	3

Chain R: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-56	26
α-helix	62-64	3
α-helix	65-88	24
α-helix	89-93	5
α-helix	99-131	33
α-helix	134-139	6
α-helix	146-161	16
α-helix	162-164	3
β-strand	170	1	10
β-strand	175	1	10
α-helix	181-184	4
α-helix	187-200	14
α-helix	202-221	20
α-helix	228-258	31
α-helix	267-288	22
α-helix	292-296	5
α-helix	298-309	12

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)
CX3C chemokine receptor 1	R	protein	361	Homo sapiens	P49238 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>7XBW_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKCTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVTAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (D), FASTA

>7XBW_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

>7XBW_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains E)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>7XBW_4 CX3C chemokine receptor 1 (chains R)
MDQFPESVTENFEYDDLAEACYIGDIVVFGTVFLSIFYSVIFAIGLVGNLLVVFALTNSK
KPKSVTDIYLLNLALSDLLFVATLPFWTHYLINEKGLHNAMCKFTTAFFFIGFFGSIFFL
TVISIDRYLAIVLAANSMNNRTVQHGVTISLGVWAAAILVAAPQFMFTKQKENECLGDYP
EVLQEIWPVLRNVETNFLGFLLPLLIMSYCYFRIIQTLFSSKNHKKAKAIKLILLVVIVF
FLFWTPYNVVIFLETLKLYDFFPSCDMRKDLRLALSVTETVAFSHCCLNPLIYAFAGEKF
RRYLYHLYGKCLAVLEFLEVLFQGPWSHPQFEKGGGSGGGSGGSAWSHPQFEKDYKDDDD
K

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	3

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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