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 

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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
  • Primary Citation of Related Structures:  
    6OB5

  • 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 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltodextrin-binding proteinB [auth A],
A [auth B]		372Escherichia coliMutation(s): 8 
Gene Names: malE, SAMEA3485101_02947
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEX9
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ankyrin Repeat Domain (AR), S3-2D variantC, D166unidentifiedMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseE, F 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FPP (Subject of Investigation/LOI)
Query on FPP
Download Ideal Coordinates CCD File 
G [auth D]FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FPP Binding MOAD:  6OB5 Kd: 6100 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001		E, Falpha-maltoseOligosaccharide / Nutrient 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

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Ligand Structure Quality Assessment 


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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  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary