5TS4

Crystal structure of a de novo designed protein with curved beta-sheet


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.005 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.274 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Principles for designing proteins with cavities formed by curved beta sheets.

Marcos, E.Basanta, B.Chidyausiku, T.M.Tang, Y.Oberdorfer, G.Liu, G.Swapna, G.V.Guan, R.Silva, D.A.Dou, J.Pereira, J.H.Xiao, R.Sankaran, B.Zwart, P.H.Montelione, G.T.Baker, D.

(2017) Science 355: 201-206

  • DOI: 10.1126/science.aah7389
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Active sites and ligand-binding cavities in native proteins are often formed by curved β sheets, and the ability to control β-sheet curvature would allow design of binding proteins with cavities customized to specific ligands. Toward this end, we inv ...

    Active sites and ligand-binding cavities in native proteins are often formed by curved β sheets, and the ability to control β-sheet curvature would allow design of binding proteins with cavities customized to specific ligands. Toward this end, we investigated the mechanisms controlling β-sheet curvature by studying the geometry of β sheets in naturally occurring protein structures and folding simulations. The principles emerging from this analysis were used to design, de novo, a series of proteins with curved β sheets topped with α helices. Nuclear magnetic resonance and crystal structures of the designs closely match the computational models, showing that β-sheet curvature can be controlled with atomic-level accuracy. Our approach enables the design of proteins with cavities and provides a route to custom design ligand-binding and catalytic sites.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
denovo NTF2
A, B, C, D
110N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download SDF File 
Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.005 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.274 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.307α = 90.00
b = 101.538β = 90.00
c = 101.584γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Defense Threat Reduction AgencyUnited StatesHDTRA 1-11-1-0041
European CommissionSpainFP7-PEOPLE-2011-IOF 298976
European CommissionAustria332094 ASR-CompEnzDes FP7-PEOPLE-2012-IOF).
Department of Energy (United States)United StatesDE-AC02-05CH11231

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-01
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence