6OB5

Computationally-designed, modular sense/response system (S3-2D)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.238 

wwPDB Validation 3D Report Full Report



Literature

Computational design of a modular protein sense-response system.

Glasgow, A.A., Huang, Y.M., Mandell, D.J., Thompson, M., Ritterson, R., Loshbaugh, A.L., Pellegrino, J., Krivacic, C., Pache, R.A., Barlow, K.A., Ollikainen, N., Jeon, D., Kelly, M.J.S., Fraser, J.S., Kortemme, T.

(2019) Science 366: 1024-1028

  • DOI: 10.1126/science.aax8780
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Sensing and responding to signals is a fundamental ability of living systems, but despite substantial progress in the computational design of new protein structures, there is no general approach for engineering arbitrary new protein sensors. Here, we ...

    Sensing and responding to signals is a fundamental ability of living systems, but despite substantial progress in the computational design of new protein structures, there is no general approach for engineering arbitrary new protein sensors. Here, we describe a generalizable computational strategy for designing sensor-actuator proteins by building binding sites de novo into heterodimeric protein-protein interfaces and coupling ligand sensing to modular actuation through split reporters. Using this approach, we designed protein sensors that respond to farnesyl pyrophosphate, a metabolic intermediate in the production of valuable compounds. The sensors are functional in vitro and in cells, and the crystal structure of the engineered binding site closely matches the design model. Our computational design strategy opens broad avenues to link biological outputs to new signals.

    Organizational Affiliation: 

    Chan Zuckerberg Biohub, San Francisco, CA, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltodextrin-binding protein
A, B
372Escherichia coliMutation(s): 8 
Gene Names: malE, SAMEA3485101_02947, BvCmsHHP001_03856
Find proteins for A0A2Y0TBT9 (Escherichia coli)
Go to UniProtKB:  A0A2Y0TBT9

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ankyrin Repeat Domain (AR), S3-2D variant
C, D
166unidentifiedMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FPP
Query on FPP
Download CCD File 
D
FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N		 Ligand Interaction
MAL
Query on MAL
Download CCD File 
A, B
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.57α = 90
b = 190.92β = 90.15
c = 55.48γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
pointlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM110089

Revision History 

  • Version 1.0: 2019-12-04
    Type: Initial release