5EWX

Fusion protein of T4 lysozyme and B4 domain of protein A from staphylococcal aureus with chemical cross-linker EY-CBS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker.

Jeong, W.H.Lee, H.Song, D.H.Eom, J.H.Kim, S.C.Lee, H.S.Lee, H.Lee, J.O.

(2016) Nat Commun 7: 11031-11031

  • DOI: 10.1038/ncomms11031
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Most of the cross linkers available have flexible spacers. Because of this, the linked hybrids have significant str ...

    Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Most of the cross linkers available have flexible spacers. Because of this, the linked hybrids have significant structural flexibility and the relative structure between their two components is largely unpredictable. Here we describe a method of connecting two proteins via a 'fusion α helix' formed by joining two pre-existing helices into a single extended helix. Because simple ligation of two helices does not guarantee the formation of a continuous helix, we used EY-CBS, a synthetic cross linker that has been shown to react selectively with cysteines in α-helices, to stabilize the connecting helix. Formation and stabilization of the fusion helix was confirmed by determining the crystal structures of the fusion proteins with and without bound EY-CBS. Our method should be widely applicable for linking protein building blocks to generate predictable structures.


    Organizational Affiliation

    Department of Chemistry, KAIST, Daejeon 34141, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endolysin,Immunoglobulin G-binding protein A,Endolysin
A, B
227Staphylococcus aureusEnterobacteria phage T4
This entity is chimeric
Mutation(s): 9 
Gene Names: spa, E
EC: 3.2.1.17
Find proteins for P38507 (Staphylococcus aureus)
Go to UniProtKB:  P38507
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EYC
Query on EYC

Download SDF File 
Download CCD File 
A, B
2,2'-ethyne-1,2-diylbis{5-[(chloroacetyl)amino]benzenesulfonic acid}
C18 H14 Cl2 N2 O8 S2
KKVZAHKPXRPKDH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.522α = 90.00
b = 149.850β = 122.69
c = 55.836γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release