9CDV | pdb_00009cdv

Crystal Structure of Rhombotarget A

• PDB DOI: https://doi.org/10.2210/pdb9CDV/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Acinetobacter terrae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-25 Released: 2025-07-02 
• Deposition Author(s): Bera, A.K., Rettie, S., Kang, A., Bhardwaj, G.
• Funding Organization(s): Defense Advanced Research Projects Agency (DARPA), Defense Threat Reduction Agency (DTRA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: in silico

Literature

Accurate de novo design of high-affinity protein-binding macrocycles using deep learning.

Rettie, S.A., Juergens, D., Adebomi, V., Bueso, Y.F., Zhao, Q., Leveille, A.N., Liu, A., Bera, A.K., Wilms, J.A., Uffing, A., Kang, A., Brackenbrough, E., Lamb, M., Gerben, S.R., Murray, A., Levine, P.M., Schneider, M., Vasireddy, V., Ovchinnikov, S., Weiergraber, O.H., Willbold, D., Kritzer, J.A., Mougous, J.D., Baker, D., DiMaio, F., Bhardwaj, G.

(2025) Nat Chem Biol 

• PubMed: 40542165 
• DOI: https://doi.org/10.1038/s41589-025-01929-w
• Primary Citation of Related Structures:  
  9CDT, 9CDU, 9CDV, 9HGC, 9HGD


• PubMed Abstract: 
  

  Developing macrocyclic binders to therapeutic proteins typically relies on large-scale screening methods that are resource intensive and provide little control over binding mode. Despite progress in protein design, there are currently no robust approaches for de novo design of protein-binding macrocycles. Here we introduce RFpeptides, a denoising diffusion-based pipeline for designing macrocyclic binders against protein targets of interest. We tested 20 or fewer designed macrocycles against each of four diverse proteins and obtained binders with medium to high affinity against all targets. For one of the targets, Rhombotarget A (RbtA), we designed a high-affinity binder (K _d  < 10 nM) despite starting from the predicted target structure. X-ray structures for macrocycle-bound myeloid cell leukemia 1, γ-aminobutyric acid type A receptor-associated protein and RbtA complexes match closely with the computational models, with a Cα root-mean-square deviation < 1.5 Å to the design models. RFpeptides provides a framework for rapid and custom design of macrocyclic peptides for diagnostic and therapeutic applications.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA.
Cancer Research @UCC, University College Cork, Cork, Ireland.
Department of Microbiology, University of Washington, Seattle, WA, USA.
Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, MA, USA.
Heinrich-Heine-Universität Düsseldorf, Institut für Physikalische Biologie, Düsseldorf, Germany.
Forschungszentrum Jülich, Institute of Biological Information Processing, Structural Biochemistry (IBI-7), Jülich, Germany.
Molecular Cell Biology of Autophagy Laboratory, The Francis Crick Institute, London, UK.
Department of Chemistry, University of Washington, Seattle, WA, USA.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Howard Hughes Medical Institute, 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. [e-mail].
Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 101.42 kDa 
• Atom Count: 7,217 
• Modeled Residue Count: 884 
• Deposited Residue Count: 930 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhombotarget A	A, B	465	Acinetobacter terrae	Mutation(s): 0
UniProt
Find proteins for A0A0D5YFQ2 (Acinetobacter baumannii) Explore A0A0D5YFQ2  Go to UniProtKB:  A0A0D5YFQ2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	F [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
MG	C [auth A], D [auth B], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.156	α = 90
b = 106.477	β = 107.04
c = 71.305	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Bera, A.K., Rettie, S., Kang, A., Bhardwaj, G.

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Funding Organization	Location	Grant Number
Defense Advanced Research Projects Agency (DARPA)	United States	--
Defense Threat Reduction Agency (DTRA)	United States	--

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release