3TCJ

CcdB dimer from V. fisheri in complex with one C-terminal domain of F-plasmid CcdA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Energetic basis of uncoupling folding from binding for an intrinsically disordered protein.

Drobnak, I.De Jonge, N.Haesaerts, S.Vesnaver, G.Loris, R.Lah, J.

(2013) J.Am.Chem.Soc. 135: 1288-1294

  • DOI: 10.1021/ja305081b

  • PubMed Abstract: 
  • Intrinsically disordered proteins (IDPs) are proteins that lack a unique three-dimensional structure in their native state. Many have, however, been found to fold into a defined structure when interacting with specific binding partners. The energetic ...

    Intrinsically disordered proteins (IDPs) are proteins that lack a unique three-dimensional structure in their native state. Many have, however, been found to fold into a defined structure when interacting with specific binding partners. The energetic implications of such behavior have been widely discussed, yet experimental thermodynamic data is scarce. We present here a thorough thermodynamic and structural study of the binding of an IDP (antitoxin CcdA) to its molecular target (gyrase poison CcdB). We show that the binding-coupled folding of CcdA is driven by a combination of specific intramolecular interactions that favor the final folded structure and a less specific set of intermolecular contacts that provide a desolvation entropy boost. The folded structure of the bound IDP appears to be defined largely by its own amino acid sequence, with the binding partner functioning more as a facilitator than a mold to conform to. On the other hand, specific intermolecular interactions do increase the binding affinity up to the picomolar range. Overall, this study shows how an IDP can achieve very strong and structurally well-defined binding and it provides significant insight into the molecular forces that enable such binding properties.


    Related Citations: 
    • Purification and crystallization of Vibrio fischeri CcdB and its complexes with fragments of gyrase and CcdA.
      De Jonge, N.,Buts, L.,Vangelooven, J.,Mine, N.,Van Melderen, L.,Wyns, L.,Loris, R.
      (2007) Acta Crystallogr.,Sect.F 63: 356


    Organizational Affiliation

    Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, 1000 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CcdB
A, B
105Aliivibrio fischeriMutation(s): 0 
Gene Names: ccdB
Find proteins for Q84B82 (Aliivibrio fischeri)
Go to UniProtKB:  Q84B82
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein CcdA
T
36Escherichia coli O157:H7Mutation(s): 0 
Gene Names: ccdA (H, letA)
Find proteins for P62553 (Escherichia coli O157:H7)
Go to UniProtKB:  P62553
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.864α = 90.00
b = 62.561β = 90.00
c = 81.951γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MAR345dtbdata collection
DENZOdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2014-10-08
    Type: Structure summary
  • Version 1.2: 2014-10-22
    Type: Database references