8BCT

X-ray crystal structure of a de novo selected helix-loop-helix heterodimer in a syn arrangement, 26alpha/26beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

Starting Model: other
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Design and Selection of Heterodimerizing Helical Hairpins for Synthetic Biology.

Smith, A.J.Naudin, E.A.Edgell, C.L.Baker, E.G.Mylemans, B.FitzPatrick, L.Herman, A.Rice, H.M.Andrews, D.M.Tigue, N.Woolfson, D.N.Savery, N.J.

(2023) ACS Synth Biol 12: 1845-1858

  • DOI: https://doi.org/10.1021/acssynbio.3c00231
  • Primary Citation of Related Structures:  
    8BCS, 8BCT

  • PubMed Abstract: 

    Synthetic biology applications would benefit from protein modules of reduced complexity that function orthogonally to cellular components. As many subcellular processes depend on peptide-protein or protein-protein interactions, de novo designed polypeptides that can bring together other proteins controllably are particularly useful. Thanks to established sequence-to-structure relationships, helical bundles provide good starting points for such designs. Typically, however, such designs are tested in vitro and function in cells is not guaranteed. Here, we describe the design, characterization, and application of de novo helical hairpins that heterodimerize to form 4-helix bundles in cells. Starting from a rationally designed homodimer, we construct a library of helical hairpins and identify complementary pairs using bimolecular fluorescence complementation in E. coli . We characterize some of the pairs using biophysics and X-ray crystallography to confirm heterodimeric 4-helix bundles. Finally, we demonstrate the function of an exemplar pair in regulating transcription in both E. coli and mammalian cells.


  • Organizational Affiliation

    School of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26alphaA [auth D],
C [auth B],
E [auth H],
H [auth F]
51synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
26betaB [auth G],
D [auth E],
F [auth A],
G [auth C]
51synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth D]
K [auth G]
M [auth B]
O [auth E]
S [auth C]
I [auth D],
K [auth G],
M [auth B],
O [auth E],
S [auth C],
U [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth D],
N [auth B],
Q [auth E],
T [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
L [auth G],
P [auth E],
R [auth A],
V [auth F]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.893α = 90
b = 78.322β = 107.97
c = 81.55γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S002820/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V006231/1
Max Planck Bristol Centre for Minimal Biology - University of BristolUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary