8IC0: CXCL8 bound C-X-C chemokine receptor 1

Cryo-EM structure of CXCL8 bound C-X-C chemokine receptor 1 in complex with Gi heterotrimer. Determined by electron microscopy at 3.41 Å resolution. Released 19 Jul 2023.

Method: Electron microscopy
Resolution: 3.41 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 9,553
Mol. weight: 163.4 kDa
Released: 19 Jul 2023

Explore 8IC0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8IC0 contains 38 α-helices and 73 β-strands across 6 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: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	36-67	32
α-helix	73-101	29
α-helix	107-139	33
α-helix	153-167	15
α-helix	169-173	5
α-helix	195-202	8
α-helix	204-207	4
α-helix	208-212	5
α-helix	213-231	19
α-helix	238-269	32
α-helix	277-296	20
α-helix	300-305	6
α-helix	310-321	12

Chain B: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	34	1	1
β-strand	36-38	3	2
α-helix	46-49	4
β-strand	185-186	2	2
β-strand	190	1	3
β-strand	195	1	3
β-strand	196	1	1
β-strand	199-200	2	2
α-helix	208-211	4
β-strand	220-222	3	2
β-strand	223-226	4	4
α-helix	232-234	3
α-helix	242-254	13
β-strand	263	1	2
β-strand	264	1	5
β-strand	266-269	4	4
α-helix	271-274	4
α-helix	283-285	3
α-helix	296-308	13
β-strand	319	1	5
α-helix	330-351	22

Chain C: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
β-strand	47-51	5	6
β-strand	58-63	6	7
β-strand	69-74	6	7
β-strand	78-83	6	7
β-strand	91-94	4	7
α-helix	95	1
β-strand	103-105	3	8
β-strand	111-114	4	8
β-strand	116	1	9
β-strand	121-125	5	8
α-helix	129-131	3
β-strand	135-139	5	8
β-strand	146	1	9
β-strand	149-153	5	10
β-strand	156-159	4	10
β-strand	165-170	6	10
β-strand	176-181	6	10
α-helix	186	1
β-strand	187-192	6	11
β-strand	198-203	6	11
β-strand	208-212	5	11
β-strand	220-222	3	11
β-strand	229-234	6	12
β-strand	240-245	6	12
β-strand	250-254	5	12
β-strand	260-262	3	12
β-strand	273-278	6	13
α-helix	280-282	3
β-strand	284-289	6	13
β-strand	296-298	3	13
β-strand	315-317	3	6
β-strand	320	1	6
β-strand	327-331	5	6
β-strand	336-339	4	6

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	8-22	15
α-helix	30-44	15
α-helix	45-47	3
α-helix	53-55	3

Chain E: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	10-12	3	15
β-strand	17-25	9	14
α-helix	29-31	3
β-strand	34-39	6	16
β-strand	46-51	6	16
α-helix	53-55	3
β-strand	58-60	3	16
β-strand	68-73	6	14
β-strand	78-84	7	14
α-helix	88-90	3
β-strand	93-95	3	16
β-strand	97	1	17
β-strand	111	1	17
β-strand	115	1	16
β-strand	117-119	3	15
α-helix	125-127	3
β-strand	129	1	18
β-strand	135-136	2	19
β-strand	143-146	4	20
β-strand	148	1	18
β-strand	154	1	21
β-strand	160	1	21
β-strand	163-167	5	22
β-strand	174-178	5	22
β-strand	182-183	2	22
β-strand	191-195	5	20
β-strand	200-204	5	20
α-helix	209-211	3
β-strand	214-218	5	22
α-helix	225	1
β-strand	231-232	2	22
β-strand	233-234	2	19

Chain F: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	24-28	5	23
β-strand	38-42	5	23
β-strand	48-49	2	23
α-helix	56-68	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-X-C chemokine receptor type 1	A	protein	358	Homo sapiens	P25024 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	345	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	80	Homo sapiens	P59768 (AlphaFold model)
scFv16	E	protein	257	Mus musculus
Interleukin-8	F	protein	72	Homo sapiens	P10145

Sequence of entity 1 (A), FASTA

>8IC0_1 C-X-C chemokine receptor type 1 (chains A)
MSNITDPQMWDFDDLNFTGMPPADEDYSPCMLETETLNKYVVIIAYALVFLLSLLGNSLV
MLVILYSRVGRSVTDVYLLNLALADLLFALTLPIWAASKVNGWIFGTFLCKVVSLLKEVN
FYSGILLLACISVDRYLAIVHATRTLTQKRHLVKFVCLGCWGLSMNLSLPFFLFRQAYHP
NNSSPVCYEVLGNDTAKWRMVLRILPHTFGFIVPLFVMLFCYGFTLRTLFKAHMGQKHRA
MRVIFAVVLIFLLCWLPYNLVLLADTLMRTQVIQESCERRNNIGRALDATEILGFLHSCL
NPIIYAFIGQNFRHGFLKILAMHGLVSKEFLARHRVTSYTSSSVNVSSNLHHHHHHHH

Sequence of entity 2 (B), FASTA

>8IC0_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (C), FASTA

>8IC0_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
GPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (D), FASTA

>8IC0_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAILGSAGSAGSA

Sequence of entity 5 (E), FASTA

>8IC0_5 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQ

Sequence of entity 6 (F), FASTA

>8IC0_6 Interleukin-8 (chains F)
SAKELRCQCIKTYSKPFHPKFIKELRVIESGPHCANTEIIVKLSDGRELCLDPKENWVQR
VVEKFLKRAENS

Primary citation

Structural basis of CXC chemokine receptor 1 ligand binding and activation. Ishimoto, N., Park, J.H., Kawakami, K. et al. Nat Commun (2023) 14:4107-4107. DOI 10.1038/s41467-023-39799-2 · PubMed

Other PDB entries of the same protein (UniProt P25024 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1ILP Cxcr-1 N-terminal peptide bound to interleukin-8
1ILQ Cxcr-1 N-terminal peptide bound to interleukin-8 (minimized mean)
2LNL Structure of human CXCR1 in phospholipid bilayers
6XMN Solution NMR CXCL8-CXCR1 N-domain complex structure

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