PDBsum entry 2bgf

Ubiquitin

PDB id: 2bgf

Contents

Protein chains

76 a.a. *

* Residue conservation analysis

PDB id:

2bgf

Name:

Ubiquitin

Title:

Nmr structure of lys48-linked di-ubiquitin using chemical shift perturbation data together with rdcs and 15n-relaxation data

Structure:

Di-ubiquitin. Chain: a, b. Synonym: ubiquitin. Engineered: yes. Other_details: isopeptide bond between gly76a and lys48b

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562

NMR struc:

10 models

Authors:

A.D.J.Van Dijk,D.Fushman,A.M.J.J.Bonvin

Key ref:

A.D.van Dijk et al. (2005). Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Proteins, 60, 367-381. PubMed id: 15937902 DOI: 10.1002/prot.20476

Date:

22-Dec-04 Release date: 31-Aug-05

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 76 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1002/prot.20476

Proteins 60:367-381 (2005)

PubMed id: 15937902

Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.

A.D.van Dijk, D.Fushman, A.M.Bonvin.

ABSTRACT

When classical, Nuclear Overhauser Effect (NOE)-based approaches fail, it is possible, given high-resolution structures of the free molecules, to model the structure of a complex in solution based solely on chemical shift perturbation (CSP) data in combination with orientational restraints from residual dipolar couplings (RDCs) when available. RDCs can be incorporated into the docking following various strategies: as direct restraints and/or as intermolecular intervector projection angle restraints (Meiler et al., J Biomol NMR 2000;16:245-252). The advantage of the latter for docking is that they directly define the relative orientation of the molecules. A combined protocol in which RDCs are first introduced as intervector projection angle restraints and at a later stage as direct restraints is shown here to give the best performance. This approach, implemented in our information-driven docking approach HADDOCK (Dominguez et al., J Am Chem Soc 2003;125:1731-1737), is used to determine the solution structure of the Lys48-linked di-ubiquitin, for which chemical shift mapping, RDCs, and (15)N-relaxation data have been previously obtained (Varadan et al., J Mol Biol 2002;324:637-647). The resulting structures, derived from CSP and RDC data, are cross-validated using (15)N-relaxation data. The solution structure differs from the crystal structure by a 20 degrees rotation of the two ubiquitin units relative to each other.

Selected figure(s)

Figure 6.
Figure 6. Result of Dyndom[47] analysis, showing the rotation of the proximal domain with respect to the distal domain when comparing the representative solution structure (black) with the crystal structure (gray). The structures are fitted on the distal domain, and secondary structure elements are indicated. Two orthogonal views are shown, corresponding to a 90° rotation around a horizontal axis in the plane of the paper. The rotation axis as determined by Dyndom is indicated in red.

Figure 7.
Figure 7. Detailed view of the interface of the Ub[2] solution structure. Residues involved in hydrophobic non-bonded contacts (ball-and-stick and transparent CPK representation) or in inter-domain hydrogen bonds or salt-bridges (ball-and-stick representation) are shown (see also Supporting Table 3S; note that for a better visualization not all contacts are shown). Dotted lines represent hydrogen bonds. The residues are labeled with one-letter residue code and residue number, followed by D or P to indicate the distal or proximal domain, respectively.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 60, 367-381) copyright 2005.

Figures were selected by the author.