7SK3

Cryo-EM structure of ACKR3 in complex with CXCL12, an intracellular Fab, and an extracellular Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of atypical chemokine receptor 3 reveal the basis for its promiscuity and signaling bias.

Yen, Y.C.Schafer, C.T.Gustavsson, M.Eberle, S.A.Dominik, P.K.Deneka, D.Zhang, P.Schall, T.J.Kossiakoff, A.A.Tesmer, J.J.G.Handel, T.M.

(2022) Sci Adv 8: eabn8063-eabn8063

  • DOI: https://doi.org/10.1126/sciadv.abn8063
  • Primary Citation of Related Structures:  
    7SK3, 7SK4, 7SK5, 7SK6, 7SK7, 7SK8, 7SK9

  • PubMed Abstract: 

    Both CXC chemokine receptor 4 (CXCR4) and atypical chemokine receptor 3 (ACKR3) are activated by the chemokine CXCL12 yet evoke distinct cellular responses. CXCR4 is a canonical G protein-coupled receptor (GPCR), whereas ACKR3 is intrinsically biased for arrestin. The molecular basis for this difference is not understood. Here, we describe cryo-EM structures of ACKR3 in complex with CXCL12, a more potent CXCL12 variant, and a small-molecule agonist. The bound chemokines adopt an unexpected pose relative to those established for CXCR4 and observed in other receptor-chemokine complexes. Along with functional studies, these structures provide insight into the ligand-binding promiscuity of ACKR3, why it fails to couple to G proteins, and its bias toward β-arrestin. The results lay the groundwork for understanding the physiological interplay of ACKR3 with other GPCRs.


  • Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Atypical chemokine receptor 3393Homo sapiensMutation(s): 0 
Gene Names: ACKR3CMKOR1CXCR7GPR159RDC1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P25106 (Homo sapiens)
Explore P25106 
Go to UniProtKB:  P25106
PHAROS:  P25106
GTEx:  ENSG00000144476 
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UniProt GroupP25106
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Stromal cell-derived factor 168Homo sapiensMutation(s): 0 
Gene Names: CXCL12SDF1SDF1ASDF1B
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P48061 (Homo sapiens)
Explore P48061 
Go to UniProtKB:  P48061
PHAROS:  P48061
GTEx:  ENSG00000107562 
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UniProt GroupP48061
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CID25 Fab light chain215Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CID25 Fab heavy chain236Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CID24 Fab light chain215Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
CID24 Fab heavy chain238Homo sapiensMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA254402
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI161880
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA221289
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL071818
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA023168
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM137505
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117372

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary