8TAC | pdb_00008tac

Designed DNA binding protein

• PDB DOI: https://doi.org/10.2210/pdb8TAC/pdb
• NAKB: 8TAC

• Classification: DE NOVO PROTEIN/DNA
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-27 Released: 2024-08-28 
• Deposition Author(s): Doyle, L., Stoddard, B.L., Glasscock, C.J., McHugh, R.P., Pecoraro, R.J.
• Funding Organization(s): National Institutes of Health/Office of the Director, National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI), Washington Research Foundation, Audacious Project at the Institute for Protein Design

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: in silico

Literature

Computational design of sequence-specific DNA-binding proteins.

Glasscock, C.J., Pecoraro, R.J., McHugh, R., Doyle, L.A., Chen, W., Boivin, O., Lonnquist, B., Na, E., Politanska, Y., Haddox, H.K., Cox, D., Norn, C., Coventry, B., Goreshnik, I., Vafeados, D., Lee, G.R., Gordan, R., Stoddard, B.L., DiMaio, F., Baker, D.

(2025) Nat Struct Mol Biol 

• PubMed: 40940539 
• DOI: https://doi.org/10.1038/s41594-025-01669-4
• Primary Citation of Related Structures:  
  8TAC


• PubMed Abstract: 
  

  Sequence-specific DNA-binding proteins (DBPs) have critical roles in biology and biotechnology and there has been considerable interest in the engineering of DBPs with new or altered specificities for genome editing and other applications. While there has been some success in reprogramming naturally occurring DBPs using selection methods, the computational design of new DBPs that recognize arbitrary target sites remains an outstanding challenge. We describe a computational method for the design of small DBPs that recognize short specific target sequences through interactions with bases in the major groove and use this method to generate binders for five distinct DNA targets with mid-nanomolar to high-nanomolar affinities. The individual binding modules have specificity closely matching the computational models at as many as six base-pair positions and higher-order specificity can be achieved by rigidly positioning the binders along the DNA double helix using RFdiffusion. The crystal structure of a designed DBP-target site complex is in close agreement with the design model and the designed DBPs function in both Escherichia coli and mammalian cells to repress and activate transcription of neighboring genes. Our method provides a route to small and, hence, readily deliverable sequence-specific DBPs for gene regulation and editing.

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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 BioSciences, Rice University, Houston, TX, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Department of Physics, University of Washington, Seattle, WA, USA.
Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Program in Genetics and Genomics, Duke University, Durham, NC, USA.
Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
Department of Bioengineering, University of Washington, Seattle, WA, USA.
Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA, USA.
Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA.
BioInnovation Institute, Copenhagen, Denmark.
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Department of Computer Science, Duke University, Durham, NC, USA.
Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
Department of Biostatics and Bioinformatics, Duke University, Durham, NC, USA.
Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.2 kDa 
• Atom Count: 1,442 
• Modeled Residue Count: 154 
• Deposited Residue Count: 162 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DBP48	A, B	70	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*CP*TP*GP*AP*CP*GP*CP*GP*A)-3')	C	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*CP*GP*CP*GP*TP*CP*AP*GP*GP)-3')	D	11	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.279 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.352	α = 90
b = 103.996	β = 99.47
c = 32.825	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
PHASER	phasing
BOS	data collection
PDB_EXTRACT	data extraction
DIALS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Doyle, L., Stoddard, B.L., Glasscock, C.J., McHugh, R.P., Pecoraro, R.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/Office of the Director	United States	S10-OD028581
National Science Foundation (NSF, United States)	United States	MFB 2226466
Howard Hughes Medical Institute (HHMI)	United States	--
Washington Research Foundation	United States	--
Audacious Project at the Institute for Protein Design	United States	--

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release
  
• Version 1.1: 2025-09-24
  Changes: Database references, Structure summary