4FL4

Scaffoldin conformation and dynamics revealed by a ternary complex from the Clostridium thermocellum cellulosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Scaffoldin Conformation and Dynamics Revealed by a Ternary Complex from the Clostridium thermocellum Cellulosome.

Currie, M.A.Adams, J.J.Faucher, F.Bayer, E.A.Jia, Z.Smith, S.P.

(2012) J.Biol.Chem. 287: 26953-26961

  • DOI: 10.1074/jbc.M112.343897

  • PubMed Abstract: 
  • Cellulosomes are multienzyme complexes responsible for efficient degradation of plant cell wall polysaccharides. The nonenzymatic scaffoldin subunit provides a platform for cellulolytic enzyme binding that enhances the overall activity of the bound e ...

    Cellulosomes are multienzyme complexes responsible for efficient degradation of plant cell wall polysaccharides. The nonenzymatic scaffoldin subunit provides a platform for cellulolytic enzyme binding that enhances the overall activity of the bound enzymes. Understanding the unique quaternary structural elements responsible for the enzymatic synergy of the cellulosome is hindered by the large size and inherent flexibility of these multiprotein complexes. Herein, we have used x-ray crystallography and small angle x-ray scattering to structurally characterize a ternary protein complex from the Clostridium thermocellum cellulosome that comprises a C-terminal trimodular fragment of the CipA scaffoldin bound to the SdbA type II cohesin module and the type I dockerin module from the Cel9D glycoside hydrolase. This complex represents the largest fragment of the cellulosome solved by x-ray crystallography to date and reveals two rigid domains formed by the type I cohesin┬Ědockerin complex and by the X module-type II cohesin┬Ědockerin complex, which are separated by a 13-residue linker in an extended conformation. The type I dockerin modules of the four structural models found in the asymmetric unit are in an alternate orientation to that previously observed that provides further direct support for the dual mode of binding. Conserved intermolecular contacts between symmetry-related complexes were also observed and may play a role in higher order cellulosome structure. SAXS analysis of the ternary complex revealed that the 13-residue intermodular linker of the scaffoldin subunit is highly dynamic in solution. These studies provide fundamental insights into modular positioning, linker flexibility, and higher order organization of the cellulosome.


    Organizational Affiliation

    Department of Biomedical and Molecular Sciences, University, Kingston, Ontario K7L 3N6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycoside hydrolase family 9
A, D, G, J
88Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)Mutation(s): 0 
Gene Names: celD
EC: 3.2.1.4
Find proteins for A3DDN1 (Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Go to UniProtKB:  A3DDN1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Scaffolding dockerin binding protein A
B, E, H, K
187Clostridium thermocellumMutation(s): 0 
Gene Names: sdbA
Find proteins for P71143 (Clostridium thermocellum)
Go to UniProtKB:  P71143
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cellulosome anchoring protein cohesin region
C, F, I, L
321Clostridium thermocellumMutation(s): 0 
Gene Names: cipA
Find proteins for Q46453 (Clostridium thermocellum)
Go to UniProtKB:  Q46453
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C, E, F, H, I, K, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C, D, F, G, I, J, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 119.374α = 90.00
b = 186.305β = 90.00
c = 191.165γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2012-07-04
    Type: Database references
  • Version 1.2: 2012-08-22
    Type: Database references