8K2X

CXCR3-DNGi complex activated by CXCL10

• PDB DOI: https://doi.org/10.2210/pdb8K2X/pdb
• EM Map EMD-36842: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Escherichia coli, Oplophorus gracilirostris
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2023-07-14 Released: 2023-11-29 
• Deposition Author(s): Jiao, H.Z., Hu, H.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure basis for the modulation of CXC chemokine receptor 3 by antagonist AMG487.

Jiao, H., Pang, B., Chiang, Y.C., Chen, Q., Pan, Q., Ren, R., Hu, H.

(2023) Cell Discov 9: 119-119

• PubMed: 38012179 
• DOI: https://doi.org/10.1038/s41421-023-00617-0
• Primary Citation of Related Structures:  
  8K2W, 8K2X

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Organizational Affiliation: 

Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 202.3 kDa 
• Atom Count: 8,900 
• Modelled Residue Count: 1,138 
• Deposited Residue Count: 1,823 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	354	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	384	Homo sapiens	Mutation(s): 0  Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873  Go to UniProtKB:  P62873
PHAROS:  P62873 GTEx:  ENSG00000078369

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,C-X-C chemokine receptor type 3,Oplophorus-luciferin 2-monooxygenase catalytic subunit	D [auth R]	657	Escherichia coli, Homo sapiens, Oplophorus gracilirostris This entity is chimeric	Mutation(s): 0  Gene Names: cybC, CXCR3, GPR9 EC: 1.13.12.13 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P49682 (Homo sapiens) Explore P49682  Go to UniProtKB:  P49682
PHAROS:  P49682 GTEx:  ENSG00000186810
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for Q9GV45 (Oplophorus gracilirostris) Explore Q9GV45  Go to UniProtKB:  Q9GV45
UniProt Groups	P0ABE7Q9GV45P49682

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
single-chain variable fragment scFv16	E [auth S]	259	Oplophorus gracilirostris	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
C-X-C motif chemokine 10	F [auth L]	98	Homo sapiens	Mutation(s): 0  Gene Names: CXCL10, INP10, SCYB10 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P02778 (Homo sapiens) Explore P02778  Go to UniProtKB:  P02778
PHAROS:  P02778 GTEx:  ENSG00000169245

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	G [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Jiao, H.Z., Hu, H.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32100963
Other private		Ganghong Young Scholar Development Fund

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release
  
• Version 1.1: 2023-12-13
  Changes: Database references