4NDL

Computational design and experimental verification of a symmetric homodimer

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.312 
  • R-Value Observed: 0.313 

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This is version 1.2 of the entry. See complete history. 


Literature

Computational design and experimental verification of a symmetric protein homodimer.

Mou, Y., Huang, P.S., Hsu, F.C., Huang, S.J., Mayo, S.L.

(2015) Proc Natl Acad Sci U S A 112: 10714-10719

  • DOI: 10.1073/pnas.1505072112
  • Primary Citation of Related Structures:  
    2MG4, 4NDL

  • PubMed Abstract: 

    • Homodimers are the most common type of protein assembly in nature and have distinct features compared with heterodimers and higher order oligomers. Understanding homodimer interactions at the atomic level is critical both for elucidating their biological mechanisms of action and for accurate modeling of complexes of unknown structure ...

    Homodimers are the most common type of protein assembly in nature and have distinct features compared with heterodimers and higher order oligomers. Understanding homodimer interactions at the atomic level is critical both for elucidating their biological mechanisms of action and for accurate modeling of complexes of unknown structure. Computation-based design of novel protein-protein interfaces can serve as a bottom-up method to further our understanding of protein interactions. Previous studies have demonstrated that the de novo design of homodimers can be achieved to atomic-level accuracy by β-strand assembly or through metal-mediated interactions. Here, we report the design and experimental characterization of a α-helix-mediated homodimer with C2 symmetry based on a monomeric Drosophila engrailed homeodomain scaffold. A solution NMR structure shows that the homodimer exhibits parallel helical packing similar to the design model. Because the mutations leading to dimer formation resulted in poor thermostability of the system, design success was facilitated by the introduction of independent thermostabilizing mutations into the scaffold. This two-step design approach, function and stabilization, is likely to be generally applicable, especially if the desired scaffold is of low thermostability.

    Organizational Affiliation: 

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 shingjonghuang@ntu.edu.tw steve@mayo.caltech.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENH-c2b, computational designed homodimerB [auth A],
A [auth B],
C		72Drosophila melanogasterMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.312 
  • R-Value Observed: 0.313 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.55α = 90
b = 167.77β = 90
c = 29.74γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references
  • Version 1.2: 2015-09-16
    Changes: Database references