PDBsum entry 1ss8

Chaperone

PDB id: 1ss8

Contents

Protein chains

(+ 1 more) 524 a.a. *

Waters ×107

* Residue conservation analysis

PDB id:

1ss8

Name:

Chaperone

Title:

Groel

Structure:

Groel protein. Chain: a, b, c, d, e, f, g. Synonym: protein cpn60, 60 kda chaperonin. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: grol, groel, mopa, b4143, c5227, z5748, ecs5124, sf4297, s4564. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Heptamer (from PDB file)

Resolution:

2.70Å R-factor: 0.216 R-free: 0.249

Authors:

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

Key ref:

C.Chaudhry et al. (2004). Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states. J Mol Biol, 342, 229-245. PubMed id: 15313620 DOI: 10.1016/j.jmb.2004.07.015

Date:

23-Mar-04 Release date: 01-Mar-05

Protein chains

P0A6F5  (CH60_ECOLI) -  Chaperonin GroEL from Escherichia coli (strain K12)

Seq: 548 a.a.

Struc: 524 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.5.6.1.7 - chaperonin ATPase.
• Reaction: ATP + H2O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2004.07.015

J Mol Biol 342:229-245 (2004)

PubMed id: 15313620

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

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

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. 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.

Selected figure(s)

Figure 4.
Figure 4. Effect of intermediate domain motion on apical domain in unliganded GroEL. For illustrative purposes, we have performed 25° clockwise and 25° counterclockwise rotations about the predominant libration axis of the intermediate domain (I1, see Figure 3). Two orthogonal views (top and bottom) of the resultant coordinates, related by a 90° vertical rotation are shown to capture the complex motion. The top views are looking approximately from a neighboring subunit in the ring, while the bottom views are from outside the ring looking towards the central 7-fold axis.

Figure 7.
Figure 7. Intermediate domain motion in the cis GroEL subunit leads to increased coupling with the equatorial domain. For illustrative purpose, we have performed 25° clockwise and 25° counterclockwise rotations about the predominant libration axis of the intermediate domain (I1, see Figure 6).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 229-245) copyright 2004.

Figures were selected by an automated process.