8YNF | pdb_00008ynf

Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8

• PDB DOI: https://doi.org/10.2210/pdb8YNF/pdb
• EM Map EMD-39423: EMDB EMDataResource

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-11 Released: 2025-09-17 
• Deposition Author(s): Banerjee, R., Khanppnavar, B., Maharana, J., Saha, S., Korkhov, V.M., Shukla, A.K.
• Funding Organization(s): Department of Biotechnology (DBT, India), Wellcome Trust, Science and Engineering Research Board (SERB)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.65 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8

Banerjee, R., Khanppnavar, B., Maharana, J., Saha, S., Korkhov, V.M., Shukla, A.K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 119.55 kDa 
• Atom Count: 4,636 
• Modeled Residue Count: 712 
• Deposited Residue Count: 1,100 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Atypical chemokine receptor 1	A [auth B], D [auth A]	392	Homo sapiens	Mutation(s): 0  Gene Names: ACKR1, DARC, FY, GPD
UniProt & NIH Common Fund Data Resources
Find proteins for Q16570 (Homo sapiens) Explore Q16570  Go to UniProtKB:  Q16570
PHAROS:  Q16570 GTEx:  ENSG00000213088

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IL-8(9-77)	B [auth D], C [auth E], E [auth G], F [auth H]	79	Homo sapiens	Mutation(s): 0  Gene Names: CXCL8, IL8
UniProt & NIH Common Fund Data Resources
Find proteins for P10145 (Homo sapiens) Explore P10145  Go to UniProtKB:  P10145
PHAROS:  P10145 GTEx:  ENSG00000169429

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.65 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.0
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Banerjee, R., Khanppnavar, B., Maharana, J., Saha, S., Korkhov, V.M., Shukla, A.K.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR29041/BRB/10/1697/2018
Wellcome Trust	United Kingdom	IA/S/20/1/504916
Science and Engineering Research Board (SERB)	India	SPR/2020/000408
Science and Engineering Research Board (SERB)	India	IPA/2020/000405

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release