PDBsum entry 1mnf

Chaperone

PDB id: 1mnf

Contents

Protein chains

(+ 8 more) 525 a.a. *

(+ 8 more) 12 a.a. *

Waters ×213

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Domain motions in groel upon binding of an oligopeptide.

Authors

J.Wang, L.Chen.

Ref.

J Mol Biol, 2003, 334, 489-499. [DOI no: 10.1016/j.jmb.2003.09.074]

PubMed id

14623189

Abstract

GroEL assists protein folding by preventing the interaction of partially folded molecules with other non-native proteins. It binds them, sequesters them, and then releases them so that they can fold in an ATP-driven cycle. Previous studies have also shown that protein substrates, GroES, and oligopeptides bind to partially overlapped sites on the apical domain surfaces of GroEL. In this study, we have determined the crystal structure at 3.0A resolution of a symmetric (GroEL-peptide)(14) complex. The binding of each of these small 12 amino acid residue peptides to GroEL involves interactions between three adjacent apical domains of GroEL. Each peptide interacts primarily with a single GroEL subunit. Residues R231 and R268 from adjacent subunits isolate each substrate-binding pocket, and prevent bound substrates from sliding into adjacent binding pockets. As a consequence of peptide binding, domains rotate and inter-domain interactions are greatly enhanced. The direction of rotation of the apical domain of each GroEL subunit is opposite to that of its intermediate domain. Viewed from outside, the apical domains rotate clockwise within one GroEL ring, while the ATP-induced apical domain rotation is counter-clockwise.

Figure 3.
Figure 3. Peptide-induced domain rotations. A, Subunit comparison in a view approximately perpendicular to the 7-fold axis. B, View along the 7-fold axis. All subunits are superimposed using equatorial domains (cyan). Subunits in the apo structure[33.] are in cyan. Domains of subunits in this structure are green and red for the intermediate and apical domains, respectively. Red and green arrows indicate the rotations of the apical and intermediate domains in this structure.

Figure 4.
Figure 4. Peptide-induced domain rotations are distinct from ATP-induced ones. A, View nearly perpendicular to the 7-fold axis. B, View along the 7-fold axis. Averaged coordinates are used for the apo structure[33.] (cyan), the KMgATP bound structure [30.] (silver), and this complex structure (apical domain, red; intermediate domain, green; and equatorial domain, cyan) with the bound peptide in yellow. Arrows indicate the rotations of both intermediate and apical domains upon binding of ATP.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 334, 489-499) copyright 2003.

Secondary reference #1

Title

The crystal structure of a groel/peptide complex: plasticity as a basis for substrate diversity.

Authors

L.Chen, P.B.Sigler.

Ref.

Cell, 1999, 99, 757-768. [DOI no: 10.1016/S0092-8674(00)81673-6]

PubMed id

10619429

Figure 4.
Figure 4. Structural Comparisons of Three Peptides Interacting with Helices H and I of the Apical DomainSBP is yellow, the GroES mobile loop ([46]) is cyan, the N-terminal extension of the apical domain ( [6]) is magenta, and helices H and I are red.(A) Superposition of Cα coordinates of the apical domain of three structures, showing the backbone of three different peptides bound over the peptide-binding groove formed by helix H and helix I. Structure of the helices displayed here is taken from the structure of the SBP/apical domain complex.(B–D) Molecular surfaces color coded by curvature (green for convex, and gray for concave) of the binding groove in SBP/apical domain, GroEL/GroES/(ADP)[7], and N-terminal extension/apical domain, respectively. The orientation in these three figures is the same as in (A). For clarity, only side chains of residues located at the C-terminal arms of the β turn of the SBP (starting from W7) and the GroES mobile loop (starting from I25) are shown, as these segments form most of the contacts with the binding site. The N-terminal arms of the β turn of these two peptides are shown as a Cα trace. Residues in the peptides that form extensive side chain interactions with the binding site are labeled.(A) was produced using MOLSCRIPT and RASTER 3D ([22 and 31]), and (B)–(D) were generated with GRASP ( [32]).

Figure 6.
Figure 6. Molecular Surface Representation of the Substrate-Binding Sites in GroELThe molecular surface of the binding sites formed by helices H and I is highlighted in red. The binding sites form “elastic rings” located on the opening of the GroEL central cavities.(A) Top view of GroEL.(B) Stereo view of the central cavities of binding-competent GroEL.The three subunits from each of the rings nearest the reader were removed to show the inside of the central cavities. Figures were generated in GRASP ([32]).

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #2

Title

The 2.4 a crystal structure of the bacterial chaperonin groel complexed with ATP gamma s.

Authors

D.C.Boisvert, J.Wang, Z.Otwinowski, A.L.Horwich, P.B.Sigler.

Ref.

Nat Struct Biol, 1996, 3, 170-177.

PubMed id

8564544

Secondary reference #3

Title

The crystal structure of the bacterial chaperonin groel at 2.8 a.

Authors

K.Braig, Z.Otwinowski, R.Hegde, D.C.Boisvert, A.Joachimiak, A.L.Horwich, P.B.Sigler.

Ref.

Nature, 1994, 371, 578-586.

PubMed id

7935790

Secondary reference #4

Title

Conformational variability in the refined structure of the chaperonin groel at 2.8 a resolution.

Authors

K.Braig, P.D.Adams, A.T.Brünger.

Ref.

Nat Struct Biol, 1995, 2, 1083-1094.

PubMed id

8846220

Secondary reference #5

Title

The crystal structure of the asymmetric groel-Groes-(Adp)7 chaperonin complex.

Authors

Z.Xu, A.L.Horwich, P.B.Sigler.

Ref.

Nature, 1997, 388, 741-750. [DOI no: 10.1038/41944]

PubMed id

9285585

Figure 1.
Figure 1 Overall architecture and dimensions of the GroEL-GroES complex. a, Van der Waals space-filling model of the entire complex in a top view looking down from the GroES-binding (cis) side; b, as a, but in a side view. The complex is colour coded as follows: trans GroEL ring, red; cis GroEL ring, green; GroES, gold. c, C drawing of the 'inside' of the GroEL-GroES complex. The view was produced by cutting the assembly open with a plane containing the 7-fold axis. ADP molecules bound to cis GroEL ring are shown as space-filling models. a, b, Produced using MidasPlus (Computer Graphics Laboratory, University of California, San Francisco); c, produced using program O53.

Figure 6.
Figure 6 Nucleotide-binding site in the cis ring of the GroEL-GroES complex. a, Stereo pair of a SigmaA-weighted 2F[o] - F[c] electron-density map contoured at 2 showing the ADP-binding pocket in a subunit of the cis GroEL ring. ADP, white, protein, yellow. 'Mg' denotes a bound magnesium ion. b, Stereo view of direct Mg2+-ADP interactions with the protein. The protein is shown as a skeletal model and is coloured as in Fig. 2. The ADP is a white ball-and-stick model, the Mg2+ is a red sphere, hydrogen bonds are shown as white dotted lines and magnesium coordinations are red dotted lines. c, Schematic representation of direct Mg2+-ADP interactions with the protein (less than 3.2 �). Amino-acid residues from the equatorial domain are blue, and those from the intermediate domain are green, as in Fig. 2. Hydrogen bonds are shown as single-arrow dashed lines, and magnesium coordinations are shown as double-arrow dashed lines. Residues interacting with ADP through van der Waals contacts are shown along a curved line. OG, OG1, OD1, OD2 and NH stand for O , O 1, O 1, O 2 and peptide NH, respectively. a, Produced using O53; b, produced using InsightII (BioSym Technology).

The above figures are reproduced from the cited reference with permission from Macmillan Publishers Ltd