8BFE

A dimeric de novo coiled-coil assembly: PK-2 (CC-TypeN-LaUbUcLd)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

De novo design of discrete, stable 3 10 -helix peptide assemblies.

Kumar, P.Paterson, N.G.Clayden, J.Woolfson, D.N.

(2022) Nature 607: 387-392

  • DOI: 10.1038/s41586-022-04868-x
  • Primary Citation of Related Structures:  
    7QDI, 7QDJ, 7QDK, 8BFD, 8BFE

  • PubMed Abstract: 
  • The α-helix is pre-eminent in structural biology 1 and widely exploited in protein folding 2 , design 3 and engineering 4 . Although other helical peptide conformations do exist near to the α-helical region of conformational space-namely, 3 10 -helices and π-helices 5 -these occur much less frequently in protein structures ...

    The α-helix is pre-eminent in structural biology 1 and widely exploited in protein folding 2 , design 3 and engineering 4 . Although other helical peptide conformations do exist near to the α-helical region of conformational space-namely, 3 10 -helices and π-helices 5 -these occur much less frequently in protein structures. Less favourable internal energies and reduced tendencies to pack into higher-order structures mean that 3 10 -helices rarely exceed six residues in length in natural proteins, and that they tend not to form normal supersecondary, tertiary or quaternary interactions. Here we show that despite their absence in nature, synthetic peptide assemblies can be built from 3 10 -helices. We report the rational design, solution-phase characterization and an X-ray crystal structure for water-soluble bundles of 3 10 -helices with consolidated hydrophobic cores. The design uses six-residue repeats informed by analysing 3 10 -helical conformations in known protein structures, and incorporates α-aminoisobutyric acid residues. Design iterations reveal a tipping point between α-helical and 3 10 -helical folding, and identify features required for stabilizing assemblies of 3 10 -helices. This work provides principles and rules to open opportunities for designing into this hitherto unexplored region of protein-structure space.


    Organizational Affiliation

    BrisSynBio, University of Bristol, Bristol, UK. d.n.woolfson@bristol.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CC-TypeN-LaUbUcLd
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
32synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
NA [auth N](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth E],
T [auth A],
Y [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth E],
EA [auth G],
FA [auth I],
IA [auth J],
AA [auth D],
BA [auth E],
EA [auth G],
FA [auth I],
IA [auth J],
LA [auth L],
QA [auth P],
RA [auth P],
W [auth B],
X [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
DA [auth F],
GA [auth J],
HA [auth J],
JA [auth K],
KA [auth K],
DA [auth F],
GA [auth J],
HA [auth J],
JA [auth K],
KA [auth K],
MA [auth N],
OA [auth P],
PA [auth P],
Q [auth A],
R [auth A],
S [auth A],
U [auth B],
V [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AIB
Query on AIB
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.891α = 90
b = 133.886β = 104.47
c = 72.634γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
Aimlessdata scaling
Arcimboldophasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L01386X/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R00661X/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release