5U35 | pdb_00005u35

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

• PDB DOI: https://doi.org/10.2210/pdb5U35/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-01 Released: 2017-01-25 
• Deposition Author(s): Oberdorfer, G., Marcos, E., Basanta, B., Chidyausiku, T.M., Sankaran, B., Zwart, P.H., Baker, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

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

• PubMed: 28082595 
• DOI: https://doi.org/10.1126/science.aah7389
• Primary Citation Related Structures: 
  5KPE, 5KPH, 5L33, 5TPH, 5TPJ, 5TRV, 5TS4, 5U35


• 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 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.
Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.
Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA.
Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA.
Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, 8010-Graz, Austria.
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA.
Joint BioEnergy Institute, Emeryville, CA 94608, USA.
Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. [e-mail].
Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 29.67 kDa 
• Atom Count: 2,125 
• Modeled Residue Count: 246 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo NTF2 with large cavity	A, B	125	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG6	I [auth B]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C12 H26 O6 DMDPGPKXQDIQQG-UHFFFAOYSA-N
PG4	H [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MXE	C [auth A], D [auth A], E [auth A], F [auth A], J [auth B]	2-METHOXYETHANOL C3 H8 O2 XNWFRZJHXBZDAG-UHFFFAOYSA-N
CL	G [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.01	α = 90
b = 33.2	β = 91.78
c = 86.59	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Oberdorfer, G., Marcos, E., Basanta, B., Chidyausiku, T.M., Sankaran, B., Zwart, P.H., Baker, D.

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-02-01
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations