1SX4

GroEL-GroES-ADP7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states.

Chaudhry, C.Horwich, A.L.Brunger, A.T.Adams, P.D.

(2004) J Mol Biol 342: 229-245

  • DOI: 10.1016/j.jmb.2004.07.015
  • Primary Citation of Related Structures:  
    1SS8, 1SVT, 1SX3, 1SX4

  • PubMed Abstract: 
  • Large rigid-body domain movements are critical to GroEL-mediated protein folding, especially apical domain elevation and twist associated with the formation of a folding chamber upon binding ATP and co-chaperonin GroES. Here, we have modeled the anisotropic displacements of GroEL domains from various crystallized states, unliganded GroEL, ATPgammaS-bound, ADP-AlFx/GroES-bound, and ADP/GroES bound, using translation-libration-screw (TLS) analysis ...

    Large rigid-body domain movements are critical to GroEL-mediated protein folding, especially apical domain elevation and twist associated with the formation of a folding chamber upon binding ATP and co-chaperonin GroES. Here, we have modeled the anisotropic displacements of GroEL domains from various crystallized states, unliganded GroEL, ATPgammaS-bound, ADP-AlFx/GroES-bound, and ADP/GroES bound, using translation-libration-screw (TLS) analysis. Remarkably, the TLS results show that the inherent motions of unliganded GroEL, a polypeptide-accepting state, are biased along the transition pathway that leads to the folding-active state. In the ADP-AlFx/GroES-bound folding-active state the dynamic modes of the apical domains become reoriented and coupled to the motions of bound GroES. The ADP/GroES complex exhibits these same motions, but they are increased in magnitude, potentially reflecting the decreased stability of the complex after nucleotide hydrolysis. Our results have allowed the visualization of the anisotropic molecular motions that link the static conformations previously observed by X-ray crystallography. Application of the same analyses to other macromolecules where rigid body motions occur may give insight into the large scale dynamics critical for function and thus has the potential to extend our fundamental understanding of molecular machines.


    Related Citations: 
    • Refinement of Macromolecular Structures by the Maximum-Likelihood Method
      Murshudov, G.N., Vagin, A.A., Dodson, E.J.
      (1997) Acta Crystallogr D Biol Crystallogr 53: 240

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
groEL protein
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M, N
524Escherichia coliMutation(s): 0 
Gene Names: groLgroELmopAb4143C5227Z5748ECS5124SF4297S4564
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12))
Explore P0A6F5 
Go to UniProtKB:  P0A6F5
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
groES proteinO, P, Q, R, S, T, U97Escherichia coliMutation(s): 0 
Gene Names: groSgroESmopBb4142C5226Z5747ECS5123SF4296S4563
UniProt
Find proteins for P0A6F9 (Escherichia coli (strain K12))
Explore P0A6F9 
Go to UniProtKB:  P0A6F9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 255.26α = 90
b = 265.25β = 90
c = 184.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2014-03-26
    Changes: Other
  • Version 1.4: 2017-10-11
    Changes: Refinement description