8K2W: CXCR3

Structure of CXCR3 complexed with antagonist AMG487. Determined by electron microscopy at 3.0 Å resolution. Released 29 Nov 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Lama glama, Escherichia coli, Homo sapiens
Chains: 2
Atoms: 3,143
Mol. weight: 77.24 kDa
Ligands: FI6, LPC, PCW, CLR
Released: 29 Nov 2023

Explore 8K2W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K2W contains 13 α-helices and 13 β-strands across 2 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 N: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	22-27	6	1
β-strand	32-39	8	2
β-strand	51-53	3	2
β-strand	59-61	3	2
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	94-95	2	3
β-strand	96-102	7	2
β-strand	110-113	4	2
β-strand	117-118	2	3

Chain R: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	55-80	26
α-helix	87-103	17
α-helix	106-114	9
α-helix	122-150	29
α-helix	151-155	5
α-helix	166-188	23
β-strand	192	1	4
β-strand	203	1	4
α-helix	209-220	12
α-helix	221-225	5
α-helix	226-243	18
α-helix	253-291	39
α-helix	298-329	32
α-helix	331-337	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nb6	N	protein	169	Lama glama
Soluble cytochrome b562,C-X-C chemokine receptor type 3,Kappa-type opioid receptor	R	protein	507	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), P41145 (AlphaFold model), P49682 (AlphaFold model)

Sequence of entity 1 (N), FASTA

>8K2W_1 Nb6 (chains N)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAMAQVQLQESGGGLVQAGESLRL
SCAASGTIFRLYDMGWYRRVSGNQRELVASITSGGSTKYGDSVKGRFTISRDNAKNTVYL
QMSSLKPEDTAVYYCNAEYRTGIWEELLDGWGQGTQVTVSSHHHHHHHH

Sequence of entity 2 (R), FASTA

>8K2W_2 Soluble cytochrome b562,C-X-C chemokine receptor type 3,Kappa-type opioid receptor (chains R)
MKTIIALSYIFCLVFADYKDDDDKGSADLEDNWETLNDNLKVIEKADNAAQVKDALTKMR
AAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQL
KTTRNAYIQKYLLVPRGSMVLEVSDHQVLNDAEVAALLENFSSSYDYGENESDSCCTSPP
CPQDFSLNFDRAFLPALYSLLFLLGLLGNGAVAAVLLSRRTALSSTDTFLLHLAVADTLL
VLTLPLWAVDAAVQWVFGSGLCKVAGALFNINFYAGALLLACISFDRYLNIVHATQLYRR
GPPARVTLTCLAVWGLCLLFALPDFIFLSAHHDERLNATHCQYNFPQVGRTALRVLQLVA
GFLLPLLVMAYCYAHILARLKSVRLLSGSREKDRNLRRITRLVVVVVVAFALCWTPYHLV
VLVDILMDLGALARNCGRESRVDVAKSVTSGLGYMHCCLNPLLYAFVGVKFRERMWMLLL
RLGCPNQRGLQRQPSSSRRDSSWSETS

Ligands and cofactors

ID	Name	Formula	Copies
FI6	N-[(1R)-1-[3-(4-ethoxyphenyl)-4-oxidanylidene-pyrido[2,3-d]pyrimidin-2-yl]ethyl…	C32 H28 F3 N5 O4	1
LPC	[1-myristoyl-glycerol-3-yl]phosphonylcholine	C22 H47 N O7 P	1
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	1
CLR	Cholesterol	C27 H46 O	1

Primary citation

Structure basis for the modulation of CXC chemokine receptor 3 by antagonist AMG487. Jiao, H., Pang, B., Chiang, Y.C. et al. Cell Discov (2023) 9:119-119. DOI 10.1038/s41421-023-00617-0 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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