1SVT

Crystal structure of GroEL14-GroES7-(ADP-AlFx)7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.808 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


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, 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 anis ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
groEL protein
A, B, C, D, E, F, G, H, I, J, K, L, M, N
524Escherichia coli (strain K12)Gene Names: groL (groEL, mopA)
Find proteins for P0A6F5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6F5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
groES protein
O, P, Q, R, S, T, U
97Escherichia coli (strain K12)Gene Names: groS (groES, mopB)
Find proteins for P0A6F9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6F9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AF3
Query on AF3

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.808 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.247 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 255.546α = 90.00
b = 266.855β = 90.00
c = 187.049γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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