8Y0N: CXCR3

Structure of CXCR3 in complex with VUF11418 and Go (Full map). Determined by electron microscopy at 3.07 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 3.07 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,691
Mol. weight: 146.96 kDa
Ligands: A1LW2
Released: 26 Feb 2025

Explore 8Y0N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y0N contains 29 α-helices and 62 β-strands across 5 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	33-39	7	1
β-strand	186-188	3	1
β-strand	191	1	1
β-strand	196-201	6	1
α-helix	209-211	3
α-helix	213-216	4
β-strand	221-227	7	1
α-helix	231-243	3
α-helix	244-255	12
β-strand	264-270	7	1
α-helix	272-281	10
α-helix	297-309	13
β-strand	319	1	1
β-strand	322-323	2	1
α-helix	332-350	19

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	6-25	20
α-helix	30-33	4
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-153	8	5
β-strand	156-161	6	5
β-strand	166-169	4	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	217-223	7	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-263	5	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-307	4	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	11-23	13
α-helix	30-43	14
α-helix	53-55	3

Chain R: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	58-79	22
α-helix	87-103	17
α-helix	106-114	9
α-helix	120-153	34
α-helix	169-189	21
β-strand	191-194	4	15
β-strand	201-204	4	15
α-helix	209-219	11
α-helix	220-225	6
α-helix	226-243	18
α-helix	250-282	33
α-helix	290-318	29
α-helix	323-334	12

Chain S: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	11-12	2	10
β-strand	18-24	7	9
α-helix	29-31	3
β-strand	33-40	8	11
β-strand	44-51	8	11
β-strand	58-60	3	11
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	111	1	11
β-strand	115-117	3	11
β-strand	118-119	2	10
β-strand	134-136	3	12
β-strand	143-147	5	13
β-strand	154	1	14
β-strand	160	1	14
β-strand	162-167	6	12
β-strand	174-177	4	12
α-helix	182	1
β-strand	183	1	12
α-helix	184	1
β-strand	192-196	5	13
β-strand	199-204	6	13
β-strand	214-219	6	12
α-helix	225	1
β-strand	226-227	2	12
β-strand	231-234	4	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(o) subunit alpha	A	protein	240	Homo sapiens	P09471 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	350	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Antibody fragment ScFv16	S	protein	248	Mus musculus
C-X-C chemokine receptor type 3	R	protein	424	Homo sapiens	P49682 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8Y0N_1 Guanine nucleotide-binding protein G(o) subunit alpha (chains A)
MGHHHHHHENLYFQGTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGADNSGKST
IVKQMKIIHGGSGGSGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIF
CVDLSDYNRMHESLMLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGP
NTYEDAAAYIQAQFESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIIIANNLRGCGLY

Sequence of entity 2 (B), FASTA

>8Y0N_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>8Y0N_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (S), FASTA

>8Y0N_4 Antibody fragment ScFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Sequence of entity 5 (R), FASTA

>8Y0N_5 C-X-C chemokine receptor type 3 (chains R)
MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSVLE
VSDHQVLNDAEVAALLENFSSSYDYGENESDSCCTSPPCPQDFSLNFDRAFLPALYSLLF
LLGLLGNGAVAAVLLSRRTALSSTDTFLLHLAVADTLLVLTLPLWAVDAAVQWVFGSGLC
KVAGALFNINFYAGALLLACISFDRYLNIVHATQLYRRGPPARVTLTCLAVWGLCLLFAL
PDFIFLSAHHDERLNATHCQYNFPQVGRTALRVLQLVAGFLLPLLVMAYCYAHILAVLLV
SRGQRRLRAMRLVVVVVVAFALCWTPYHLVVLVDILMDLGALARNCGRESRVDVAKSVTS
GLGYMHCCLNPLLYAFVGVKFRERMWMLLLRLGCPNQRGLQRQPSSSRRDSSWSETSEAS
YSGL

Ligands and cofactors

ID	Name	Formula	Copies
A1LW2	[(1~{R},5~{S})-6,6-dimethyl-2-bicyclo[3.1.1]hept-2-enyl]methyl-[[4-(2-iodanylph…	C25 H31 I N	1

Primary citation

Structural visualization of small molecule recognition by CXCR3 uncovers dual-agonism in the CXCR3-CXCR7 system. Saha, S., Sano, F.K., Sharma, S. et al. Nat Commun (2025) 16:3047-3047. DOI 10.1038/s41467-025-58264-w · PubMed

Other PDB entries of the same protein (UniProt P09471 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BSB 2.32 Å, Global reconstruction of DRD2 bound to LSD in complex with a mini-GoA and scFv16…
9VJE 2.47 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with buspirone
9K20 2.65 Å, Cryo-EM structure of ATP-bound P2Y purinoceptor 2-miniGo-scFv16 complex
9VJ5 2.69 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with gepirone
8E9X 2.7 Å, CryoEM structure of miniGo-coupled hM4Di in complex with DCZ
9T88 2.74 Å, Cryo-EM structure of ESG-2-37-bound D3 dopamine receptor with mini-Go
9VNF 2.74 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with (S)-pindolol
8YN7 2.77 Å, Cryo-EM structure of histamine H3 receptor in complex with immethridine and miniGo
8YN8 2.77 Å, Cryo-EM structure of histamine H3 receptor in complex with proxyfan and miniGo
9KVP 2.79 Å, Structure of SB290157 bound to human C3aR in complex with Go (Full map)
7W2Z 2.8 Å, Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go complex
8XXH 2.8 Å, Structure of CXCR2 bound to CXCL2 (CXCR2-CXCL2-Go Full map)

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