22XC | pdb_000022xc

Structure of CXCR4 in complex with a de-novo designed mini-protein antagonist

• PDB DOI: https://doi.org/10.2210/pdb22XC/pdb
• EM Map EMD-68747: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2026-01-26 Released: 2026-04-22 
• Deposition Author(s): Banerjee, R., Ganguly, M., Banerjee, N., Tiwari, D., Muratspahic, E., Baker, D., Shukla, A.K.
• Funding Organization(s): Science and Engineering Research Board (SERB), Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

De novo design of miniproteins targeting GPCRs.

Muratspahic, E., Feldman, D., Kim, D.E., Qu, X., Bratovianu, A.M., Rivera-Sanchez, P., Voss, J.H., Hertz, E.P.T., Jeppesen, M., Dimitri, F., Sakamoto, K., Nallathambi, A., Peceli, P., Cao, J., Cary, B.P., Belousoff, M.J., Keov, P., Trinh, P.N.H., Chen, Q., Ren, Y., Fine, J., Mishra, S., Dalal, A., Sinha, S., Banerjee, R., Ganguly, M., Karuppusamy, K.V., Sappington, I., Schlichthaerle, T., Zhang, J.Z., Pillai, A., Coventry, B., Mihaljevic, L., Bauer, M., Torres, S.V., Motmaen, A., Lee, G.R., Tran, L., Wang, X., Goreshnik, I., Vafeados, D.K., Svendsen, J.E., Hosseinzadeh, P., Lindegaard, N., Brandt, M., Waltenspuhl, Y., Deibler, K., Deweid, L., Bennett, A., Schoppe, J., Dong, T., Yan, X., Oostdyk, L., Cao, W., Anantharaman, L., Weisser, J.J., Bastlund, J.F., Bundgaard, C., Asuni, A.A., English, J.G., Stewart, L., Halloran, L., Spangler, J.B., Lieber, A., Shukla, A.K., Sexton, P.M., Roth, B.L., Krumm, B.E., Wootten, D., Tate, C.G., Norn, C., Baker, D.

(2026) Nature 

• PubMed: 42168559 
• DOI: https://doi.org/10.1038/s41586-026-10656-8
• Primary Citation Related Structures: 
  22XC


• PubMed Abstract: 
  

  G protein-coupled receptors (GPCRs) play key roles in physiology and are central targets for drug discovery and development ^1,2 , but the design of protein agonists and antagonists has been challenging as GPCRs are integral membrane proteins and conformationally dynamic ^3-6 . Here we describe computational de novo design methods and a high-throughput "receptor diversion" microscopy-based screen for generating GPCR binding miniproteins with high affinity, potency and selectivity. We design miniprotein agonists that activate receptors involved in itch and pain, as well as antagonists that inhibit receptors implicated in cancer, metabolic disorders such as diabetes and obesity, and migraine. Cryo-electron microscopy (cryo-EM) structures of five receptor-bound designs are close to the computational design models. A designed chemokine receptor antagonist mobilizes hematopoietic stem and progenitor cells in vivo at a level comparable to a clinically used drug, with fewer adverse effects.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
BioInnovation Institute, Copenhagen N, Denmark.
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Skape Bio ApS, Copenhagen N, Denmark.
Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
NIMH Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia.
ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia.
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA.
Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD, USA.
Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India.
University of Washington, Department of Medicine, Division of Medical Genetics, Seattle, WA, USA.
Department of Chemical Engineering, University of Washington, Seattle, WA, USA.
Department of Bioengineering, Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR, USA.
Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA.
Novo Nordisk A/S, Måløv, Denmark.
Novo Nordisk Research Centre China, Changping District, Beijing, China.
LeadHunter Services, Eurofins DiscoverX, LLC, Fremont, CA, USA.
H. Lundbeck A/S, Global Research, Copenhagen-Valby, Denmark.
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
BioInnovation Institute, Copenhagen N, Denmark. [e-mail].
Skape Bio ApS, Copenhagen N, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 170.24 kDa 
• Atom Count: 8,623 
• Modeled Residue Count: 1,040 
• Deposited Residue Count: 1,485 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dCX001 binder antagonist	A, B, D	87	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-X-C chemokine receptor type 4	C, E [auth G], F [auth R]	408	Homo sapiens	Mutation(s): 0  Gene Names: CXCR4
UniProt & NIH Common Fund Data Resources
Find proteins for P61073 (Homo sapiens) Explore P61073  Go to UniProtKB:  P61073
PHAROS:  P61073 GTEx:  ENSG00000121966

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D21 (Subject of Investigation/LOI)	H [auth C], J [auth G], L [auth R]	(2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate C37 H71 O8 P OPVZUEPSMJNLOM-PGUFJCEWSA-N
CLR (Subject of Investigation/LOI)	G [auth C], I [auth G], K [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.28 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-22 
Deposition Author(s): Banerjee, R., Ganguly, M., Banerjee, N., Tiwari, D., Muratspahic, E., Baker, D., Shukla, A.K.

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Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	IPA/2020/000405
Wellcome Trust	United Kingdom	IA/S/20/1/504916
Science and Engineering Research Board (SERB)	India	CRG/2022/002646

Revision History  

• Version 1.0: 2026-04-22
  Type: Initial release
  
• Version 1.1: 2026-06-03
  Changes: Data collection, Database references