7RG7

Crystal structure of nanoclamp8:VHH in complex with MTX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.152 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design of a methotrexate-controlled chemical dimerization system and its use in bio-electronic devices.

Guo, Z.Smutok, O.Johnston, W.A.Walden, P.Ungerer, J.P.J.Peat, T.S.Newman, J.Parker, J.Nebl, T.Hepburn, C.Melman, A.Suderman, R.J.Katz, E.Alexandrov, K.

(2021) Nat Commun 12: 7137-7137

  • DOI: https://doi.org/10.1038/s41467-021-27184-w
  • Primary Citation of Related Structures:  
    7RG7, 7RGA

  • PubMed Abstract: 

    Natural evolution produced polypeptides that selectively recognize chemical entities and their polymers, ranging from ions to proteins and nucleic acids. Such selective interactions serve as entry points to biological signaling and metabolic pathways. The ability to engineer artificial versions of such entry points is a key goal of synthetic biology, bioengineering and bioelectronics. We set out to map the optimal strategy for developing artificial small molecule:protein complexes that function as chemically induced dimerization (CID) systems. Using several starting points, we evolved CID systems controlled by a therapeutic drug methotrexate. Biophysical and structural analysis of methotrexate-controlled CID system reveals the critical role played by drug-induced conformational change in ligand-controlled protein complex assembly. We demonstrate utility of the developed CID by constructing electrochemical biosensors of methotrexate that enable quantification of methotrexate in human serum. Furthermore, using the methotrexate and functionally related biosensor of rapamycin we developed a multiplexed bioelectronic system that can perform repeated measurements of multiple analytes. The presented results open the door for construction of genetically encoded signaling systems for use in bioelectronics and diagnostics, as well as metabolic and signaling network engineering.


  • Organizational Affiliation

    ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
nano CLostridial Antibody Mimetic Protein 8 VHH306synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.152 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.121α = 90
b = 95.882β = 90
c = 118.096γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP160100973
Australian Research Council (ARC)AustraliaDP150100936
Canada Excellence Research Chair AwardCanadaCE200100029
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1113262

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-22
    Type: Initial release
  • Version 1.1: 2022-07-06
    Changes: Source and taxonomy
  • Version 1.2: 2023-10-18
    Changes: Author supporting evidence, Data collection, Refinement description