7S5B

Unbound State of a De novo designed Protein Binder to the Human Interleukin-7 Receptor

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

  • Deposited: 2021-09-10 Released: 2022-05-11 
  • Deposition Author(s): Walsh, S.T.R., Cao, L., Baker, D.
  • Funding Organization(s): Department of Defense (DOD, United States), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

Starting Model: other
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Design of protein-binding proteins from the target structure alone.

Cao, L.Coventry, B.Goreshnik, I.Huang, B.Sheffler, W.Park, J.S.Jude, K.M.Markovic, I.Kadam, R.U.Verschueren, K.H.G.Verstraete, K.Walsh, S.T.R.Bennett, N.Phal, A.Yang, A.Kozodoy, L.DeWitt, M.Picton, L.Miller, L.Strauch, E.M.DeBouver, N.D.Pires, A.Bera, A.K.Halabiya, S.Hammerson, B.Yang, W.Bernard, S.Stewart, L.Wilson, I.A.Ruohola-Baker, H.Schlessinger, J.Lee, S.Savvides, S.N.Garcia, K.C.Baker, D.

(2022) Nature 605: 551-560

  • DOI: https://doi.org/10.1038/s41586-022-04654-9
  • Primary Citation of Related Structures:  
    7N1J, 7N1K, 7N3T, 7OPB, 7RDH, 7S5B

  • PubMed Abstract: 

    The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge 1-5 . Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder-target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein-protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Miniprotein Binder
A, B
55synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: H 3 2
  • Diffraction Data: https://doi.org/10.18430/M37S5B
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.226α = 90
b = 92.226β = 90
c = 108.436γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesFA8750-17-C-0219
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700059C
Howard Hughes Medical Institute (HHMI)United StatesDB
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesACB-12002
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAGM-12006, P30GM138396
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10 OD012289

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release
  • Version 1.1: 2022-05-18
    Changes: Database references
  • Version 1.2: 2022-05-25
    Changes: Database references
  • Version 1.3: 2024-04-03
    Changes: Data collection, Refinement description