8K2X | pdb_00008k2x

CXCR3-DNGi complex activated by CXCL10

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 8K2X

This is version 1.3 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1038/s41421-023-00617-0
  • Primary Citation Related Structures: 
    8K2W, 8K2X
    • Organizational Affiliation: 
    • Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong, China.

Macromolecule Content 

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

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
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 Groups
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UniProt GroupP63096
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1384Homo sapiensMutation(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 
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UniProt GroupP62873
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Reference Sequence
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]71Homo sapiensMutation(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 
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UniProt GroupP59768
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Reference Sequence
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,C-X-C chemokine receptor type 3,Oplophorus-luciferin 2-monooxygenase catalytic subunitD [auth R]657Escherichia 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 P0ABE7 (Escherichia coli)
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Go to UniProtKB:  P0ABE7
Find proteins for P49682 (Homo sapiens)
Explore P49682 
Go to UniProtKB:  P49682
PHAROS:  P49682
GTEx:  ENSG00000186810 
Find proteins for Q9GV45 (Oplophorus gracilirostris)
Explore Q9GV45 
Go to UniProtKB:  Q9GV45
Entity Groups
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UniProt GroupsP0ABE7Q9GV45P49682
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
single-chain variable fragment scFv16E [auth S]259Oplophorus gracilirostrisMutation(s): 0 
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|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
C-X-C motif chemokine 10F [auth L]98Homo sapiensMutation(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 
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UniProt GroupP02778
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR

Query on CLR


Download:Ideal Coordinates CCD File
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 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32100963
Other privateGanghong Young Scholar Development Fund

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-07-16
    Changes: Data collection