4FL4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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
  • Primary Citation of Related Structures:  
    4FL4

  • 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 enzymes ...

    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·dockerin complex and by the X module-type II cohesin·dockerin 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycoside hydrolase family 9A, D, G, J88Acetivibrio thermocellusMutation(s): 0 
Gene Names: Cther_2220
EC: 3.2.1.4
UniProt
Find proteins for A3DDN1 (Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore A3DDN1 
Go to UniProtKB:  A3DDN1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Scaffolding dockerin binding protein AB, E, H, K187Acetivibrio thermocellusMutation(s): 0 
Gene Names: sdbA
UniProt
Find proteins for P71143 (Hungateiclostridium thermocellum)
Explore P71143 
Go to UniProtKB:  P71143
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cellulosome anchoring protein cohesin regionC, F, I, L321Acetivibrio thermocellusMutation(s): 0 
Gene Names: ClothDRAFT_2952cipA
UniProt
Find proteins for Q46453 (Hungateiclostridium thermocellum)
Explore Q46453 
Go to UniProtKB:  Q46453
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , BB [auth H] , BC [auth L] , CA [auth C] , CB [auth H] , CC [auth L] , DB [auth H] , 
AA [auth C],  BA [auth C],  BB [auth H],  BC [auth L],  CA [auth C],  CB [auth H],  CC [auth L],  DB [auth H],  DC [auth L],  EB [auth H],  EC [auth L],  FA [auth E],  FB [auth H],  FC [auth L],  GA [auth E],  GB [auth H],  GC [auth L],  HA [auth E],  HB [auth H],  HC [auth L],  IA [auth E],  JA [auth E],  KA [auth E],  KB [auth I],  LA [auth E],  LB [auth I],  MB [auth I],  NB [auth I],  O [auth B],  OA [auth F],  OB [auth I],  P [auth B],  PA [auth F],  PB [auth I],  Q [auth B],  QA [auth F],  R [auth B],  RA [auth F],  S [auth B],  SA [auth F],  SB [auth K],  T [auth B],  TA [auth F],  TB [auth K],  UA [auth F],  UB [auth K],  VA [auth F],  VB [auth K],  W [auth C],  WA [auth F],  WB [auth K],  X [auth C],  XA [auth F],  XB [auth K],  Y [auth C],  YA [auth F],  YB [auth K],  Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AB [auth G] , AC [auth L] , DA [auth D] , EA [auth D] , IB [auth I] , JB [auth I] , M [auth A] , MA [auth F] , 
AB [auth G],  AC [auth L],  DA [auth D],  EA [auth D],  IB [auth I],  JB [auth I],  M [auth A],  MA [auth F],  N [auth A],  NA [auth F],  QB [auth J],  RB [auth J],  U [auth C],  V [auth C],  ZA [auth G],  ZB [auth L]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.374α = 90
b = 186.305β = 90
c = 191.165γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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